Background: Mature spermatozoa contain numerous epididymal and seminal plasma proteins, which full identification through high-throughput technologies may allow for a better understanding of the sperm biology. Therefore, we conducted a global proteomic analysis of boar spermatozoa through shotgun and gel-based methodologies. Results: The total proteins were extracted from mature spermatozoa and subjecsted to proteome analyses. Functional analyses of gene ontology representations and pathway enrichments were conducted on the shotgun dataset, followed by immunology and gene expression validations. Shotgun and gel-based approaches allowed the detection of 2728 proteins and 2123 spots, respectively. Approximately 38% and 59% of total proteins were respectively fully and partially annotated, and 3% were unknown. Gene ontology analysis indicated high proportions of proteins associated with intracellular and cytoplasm localizations, protein and nucleic acid binding, hydrolase and transferase activities, and cellular, metabolic, and regulation of biological processes. Proteins associated with phosphorylation processes and mitochondrial membranes, nucleic acid binding, and phosphate and phosphorous metabolics represented 77% of the dataset. Pathways associated with oxidative phosphorylation, citrate cycle, and extra-cellular matrix-receptor interaction were significantly enriched. Protein complex, intracellular organelle, cytoskeletal parts, fertilization and reproduction, and gap junction pathway were significantly enriched within the top 116 highly abundant proteins. Nine randomly selected protein candidates were confirmed with gel-based identification, immunofluorescence detection, and mRNA expression. Conclusions: This study offers an in-depth proteomic mapping of mature boar spermatozoa that will enable comparative and discovery research for the improvement of male fertility.
De Abrew Abeysundara P, Dhowlaghar N, Nannapaneni R, Schilling MW, Mahmoud B, Sharma CS, Ma DP (2018) Salmonella enterica growth and biofilm formation in flesh and peel cantaloupe extracts on four food-contact surfaces. International Journal of Food Microbiology 280: 17-26.
Salmonella enterica is responsible for the highest number of foodborne disease outbreaks pertaining to cantaloupe industry. The objective of this study was to examine the growth and biofilm formation by outbreak strains of S. enterica ser. Poona (S. Poona), S. enterica ser. Stanley (S. Stanley) and S. enterica ser. Montevideo (S. Montevideo) on different food-contact processing surfaces in cantaloupe flesh and peel extracts at 22 °C and 10 °C. The generation time of all S. enterica strains tested was shorter in the high concentration (50 mg/ml) of cantaloupe extract and high temperature. In 50 mg/ml of cantaloupe flesh or peel extract, the populations of S. enterica were increased by 5 log CFU/ml in 24 h at 22 °C and 1 log CFU/ml in 72 h at 10 °C. In 2 mg/ml of cantaloupe flesh or peel extracts, the populations of S. enterica were increased by 3.5 log CFU/ml in 56 h at 22 °C, but there were no changes in 72 h at 10 °C. The biofilm production of S. enterica was greater at 50 mg/ml of cantaloupe extract and 22 °C, but no major differences (P ≥ 0.05) were found among the strains tested. In 50 mg/ml cantaloupe extract, S. enterica produced 5-6 log CFU/cm2 biofilm in 4-7 d at 22 °C and approximately 3.5-4 log CFU/cm2 in 7 d at 10 °C. In 2 mg/ml of cantaloupe extract, S. enterica produced 4-4.5 log CFU/cm2 biofilms in 4-7 d at 22 °C and 3 log CFU/cm2 in 7 d at 10 °C. Biofilm formation by S. Poona (01A4754) was lowest on buna-n rubber compared to stainless steel, polyethylene and polyurethane surfaces under the majority of conditions tested. Overall, these findings show that S. enterica strains can grow rapidly and form biofilms on different cantaloupe processing surfaces in the presence of low concentrations of cantaloupe flesh or peel extracts.
Perera D, Magbanua ZV, Thummasuwan S, Mukherjee D, Arick M 2nd, Chouvarine P, Nairn CJ, Schmutz J, Grimwood J, Dean JFD, Peterson DG (2018) Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis. Gene 663: 165-177.
Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the LP genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production.
Guy EL, Li MH, Allen PJ (2018) Effects of dietary protein levels on growth and body composition of juvenile (age-1) Black Buffalo Ictiobus niger. Aquaculture 492: 67-72.
Populations of Black Buffalo Ictiobus niger, a broadly-distributed catostomid species native to the Mississippi River basin, are in decline, similar to many other catostomids. Artificial propagation and culture are frequently a part of native species recovery plans, and developing formulated diets is a critical component of these plans. However, studies establishing protein requirements for catostomids are limited, particularly for larger juvenile to sub-adult sizes, even though catostomids are commonly reared to these sizes. Therefore, we conducted a 10-week growth study to evaluate optimal protein levels in juvenile (age-1) Black Buffalo (mean ± SE: total length = 218.7 ± 0.8 mm, weight = 148.5 ± 1.6 g). Five practical diets were formulated to contain 30, 34, 38, 41, and 45% crude protein with each diet fed to four replicate tanks (400-L) containing 10 fish each. Fish fed a diet containing 41% crude protein had greater biomass gain (total weight gain for all fish in the tank) when compared to other diets. Individual weight gain (percent increase) was greater in fish fed diets containing 41% and 45% protein compared to lower protein diets. Results from this study suggest a diet with 41% crude protein would produce optimal growth for juvenile (age-1) Black Buffalo.
Wilson AE, Sparks DL, Knott KK, Kouba AJ, Willard S, Brown A (2018) Behavioral, semiochemical and androgen responses by male giant pandas to the olfactory sexual receptivity cues of females. Theriogenology 114: 330-337.
Male giant pandas identify female sexual receptivity through the detection of olfactory cues in estrous urine. However, it is yet unknown which specific days of the female estrous cycle may provoke male sexual-social responses and a physiological readiness to mate. We hypothesized that female urine from specific days of the estrous cycle will be positively associated with specific changes in male behaviors, urinary semiochemical production, and steroidogenic activity. Experimental simultaneous choice trials were conducted in captivity with four malegiant pandas during the spring breeding season and during fall. Male interest was determined by a behavioral preference toward peri-estrual urine collected from a specific day of the estrous cycle encompassing proestrus (Day -13, Day -6, Day -3, Day -2), estrus (Day -1 and Day 0), and metestrus (Day four and Day nine) over that of anestrous urine. Provocation of male sexual motivation was examined by changes in urinary semiochemical composition and urinary androgen concentrations. During the spring, male investigative behaviors indicated a preference for Day -13, Day -3 and Day 0 urine over anestrous urine, while no significant preferences for estrous urine could be detected during fall. The relative abundance of only three compounds in male urine were significantly higher above baseline values after males were exposed to peri-estrual urine during spring; whereas 34 compounds significantly increased in the fall. Similarly, androgen concentrations increased above baseline in only two out of four males during spring, while all males had elevated androgen concentrations after exposure to Day -3 urine during the fall. Our results suggest that peri-estrual urine from Day -13, Day -3, and Day 0 elicited the greatest duration of maleinvestigation, changes in the semiochemical profile, and elevations in androgen levels. These data suggest that managers should incorporate a combination of behavioral, semiochemical, and endocrinological assessment of males in the reproductive management of giant pandas to determine impending ovulation and pinpoint the best time for male-female introductions and artificial inseminations.
Ferguson L, Luo K, Olivier AK, Cunningham FL, Blackmon S, Hanson-Dorr K, Sun H, Baroch J, Lutman MW, Quade B, Epperson W, Webby R, DeLiberto TJ, Wan XF (2018) Influenza D Virus Infection in Feral Swine Populations, United States. Emerging Infectious Diseases 24: 1020-1028.
Influenza D virus (IDV) has been identified in domestic cattle, swine, camelid, and small ruminant populations across North America, Europe, Asia, South America, and Africa. Our study investigated seroprevalence and transmissibility of IDV in feral swine. During 2012-2013, we evaluated feral swine populations in 4 US states; of 256 swine tested, 57 (19.1%) were IDV seropositive. Among 96 archived influenza A virus-seropositive feral swine samples collected from 16 US states during 2010-2013, 41 (42.7%) were IDV seropositive. Infection studies demonstrated that IDV-inoculated feral swine shed virus 3-5 days postinoculation and seroconverted at 21 days postinoculation; 50% of in-contact naive feral swine shed virus, seroconverted, or both. Immunohistochemical staining showed viral antigen within epithelial cells of the respiratory tract, including trachea, soft palate, and lungs. Our findings suggest that feral swine might serve an important role in the ecology of IDV.
Kanapeckas KL, Tseng TM, Vigueira CC, Ortiz A, Bridges WC, Burgos NR, Fischer AJ, Lawton-Rauh A (2018) Contrasting patterns of variation in weedy traits and unique crop features in divergent populations of US weedy rice (Oryza sativa sp.) in Arkansas and California. Pest Management Science 74(6): 1404-1415.
BACKGROUND: Weed evolution from crops involves changes in key traits, but it is unclear how genetic and phenotypic variation contribute to weed diversification and productivity. Weedy rice is a conspecific weed of rice (Oryza sativa) worldwide. We used principal component analysis and hierarchical clustering to understand how morphologically and evolutionarily distinct US weedy rice populations persist in rice fields in different locations under contrasting management regimes. Further, we used a representative subset of 15 sequence-tagged site fragments of expressed genes from global Oryza to assess genome-wide sequence variation among populations. RESULTS: Crop hull color and crop-overlapping maturity dates plus awns, seed (panicle) shattering (> 50%), pigmented pericarp and stature variation (30.2% of total phenotypic variance) characterize genetically less diverse California weedy rice. By contrast, wild-like hull color, seed shattering (> 50%) and stature differences (55.8% of total phenotypic variance) typify genetically diverse weedy rice ecotypes in Arkansas. CONCLUSION: Recent de-domestication of weedy species -- such as in California weedy rice -- can involve trait combinations indistinguishable from the crop. This underscores the need for strict seed certification with genetic monitoring and proactive field inspection to prevent proliferation of weedy plant types. In established populations, tillage practice may affect weed diversity and persistence over time.
Gastal GDA, Aguiar FLN, Rodrigues APR, Scimeca JM, Apgar GA, Banz WJ, Feugang JM, Gastal EL (2018) Cryopreservation and in vitro culture of white-tailed deer ovarian tissue. Theriogenology 113: 253-260.
The aims of this study were to evaluate (1) the survivability of white-tailed deer ovarian tissue after cryopreservation by slow-freezing (SF) and vitrification (VIT) techniques and in vitro culture (IVC) for up to 7 days, and (2) the effects of cryopreservation techniques on protein expression of proliferative and apoptotic markers of ovarian tissue pre- and post-in vitro culture. Ovaries (n=14) of seven white-tailed deerfawns (<1.5 years old) were used. Ovarian cortexes were cut into fragments (2 x 2 x 0.5 mm) and split into nine treatment groups: (1) fresh noncultured control, (2) fresh-IVC 1 day, (3) fresh-IVC 7 days, (4) SF noncultured, (5) SF-IVC 1 day, (6) SF-IVC 7 days, (7) VIT noncultured, (8) VIT-IVC 1 day, and (9) VIT-IVC 7 days. Preantral follicle morphology, class distribution, and density; stromal cell density; EGFR, Ki-67, Bax, and Bcl-2 protein expression; and DNA fragmentation were assessed. Results showed that: (i) white-tailed deer fresh ovarian tissue can be cultured for up to 7 days, preserving the tissue integrity and 50% of morphologically normal preantral follicles; (ii) cryopreservation of white-tailed deer ovarian tissue by either slow-freezing or vitrification does not disrupt markers of proliferation and apoptosis after thawing; (iii) ovarian fragments cryopreserved by the vitrification method had greater follicle viability during in vitro culture than the slow-freezing method; and (iv) fragments cryopreserved by slow-freezing suffered apoptosis earlier than those preserved by vitrification. The findings herein reported advance knowledge towards development of adequate cryopreservation protocols for long-term banking programs for Cervidae species.
Omer AR, Miranda LE,Moore MT,Krutz LJ, Czarnecki JMP, Kroger R, Baker BH, Hogue J, Allen PJ (2018) Reduction of solids and nutrient loss from agricultural land by tailwater recovery systems. Journal of Soil and Water Conservation 73: 284-297.
Best management practices are being implemented throughout the Lower Mississippi River Alluvial Valley with the aim of alleviating pressures placed on downstream aquatic systems by sediment and nutrient losses from agricultural land; however, research evaluating the performance of tailwater recovery (TWR) systems, an increasingly important practice, is limited. This study evaluated the ability of TWR systems to retain sediment and nutrients draining from agricultural landscapes. Composite flow-based samples were collected during flow events (precipitation or irrigation) over a two-year period in six TWR systems. Performance was evaluated by comparing concentrations and loads in water entering TWR systems (i.e., runoff or influent) from agricultural fields to water overflow exiting TWR systems (effluent). Tailwater recovery systems did not reduce concentrations of solids and nutrients, but did reduce loads of solids, phosphorus (P), and nitrogen (N) by 43%, 32%, and 44%, respectively. Annual mean load reductions were 1,142 kg solids, 0.7 kg of P, and 3.8 kg of N. Performance of TWR systems was influenced by effluent volume, system fullness, time since the previous event, and capacity of the TWR system. Mechanistically, TWR systems retain runoff on the agricultural landscape, thereby reducing the amount of sediment and nutrients entering downstream waterbodies. System performance can be improved through manipulation of influential parameters.
Krupovic M, Blomberg J, Coffin JM, Dasgupta I, Fan H, Geering AD, Gifford R, Harrach B, Hull R, Johnson W, Kreuze JF, Lindemann D, Llorens C, Lockhart B, Mayer J, Muller E, Olszewski NE, Pappu HR, Pooggin MM, Richert-Poggeler KR, Sabanadzovic S, Sanfacon H, Schoelz JE, Seal S, Stavolone L, Stoye JP, Teycheney PY, Tristem M, Koonin EV, Kuhn JH (2018) Ortervirales: New Virus Order Unifying Five Families of Reverse-Transcribing Viruses. Journal of Virology 92(12): e00515-18.
van den Burg MP, Meirmans PG, van Wagensveld TP, Kluskens B, Madden H, Welch ME, Breeuwer JAJ (2018) The Lesser Antillean Iguana (Iguana delicatissima) on St. Eustatius: Genetically Depauperate and Threatened by Ongoing Hybridization. Journal of Heredity 109(4): 426-437.
The Lesser Antillean Iguana (Iguana delicatissima) is an endangered species threatened by habitat loss and hybridization with non-native Green Iguanas (Iguana iguana). Iguana delicatissima has been extirpated on several islands, and the Green Iguana has invaded most islands with extant populations. Information is essential to protect this species from extinction. We collected data on 293 iguanas including 17 juveniles from St. Eustasius, one of the few remaining I. delicatissima strongholds. Genetic data were leveraged to test for hybridization presence with the Green Iguana using both mitochondrial and nuclear genes, including 16 microsatellite loci. The microsatellites were also analyzed to estimate genetic diversity, population structure, and effective population size. Using molecular and morphological data, we identifed 286 I. delicatissima individuals captured during our frst feldwork effort, and 7 non-native iguanas captured during a second effort, showing hybridization occurs within this population. Comparing homologous microsatellites used in studies on Dominica and Chancel, the I. delicatissima population on St. Eustatius has extremely low genetic diversity (HO = 0.051; HE = 0.057), suggesting this population is genetically depauperate. Furthermore, there is signifcant evidence for inbreeding (FIS = 0.12) and weak spatial genetic structure (FST = 0.021, P = 0.002) within this population. Besides immediate threats including hybridization, this population's low genetic diversity, presence of physiological abnormalities and low recruitment could indicate presence of inbreeding depression that threatens its long-term survival. We conclude there is a continued region-wide threat to I. delicatissima and highlight the need for immediate conservation action to stop the continuing spread of Green Iguanas and to eliminate hybridization from St. Eustatius.
Thrash A, Arick M 2nd, Peterson DG (2018) Quack: A quality assurance tool for high throughput sequence data. Analytical Biochemistry 548: 38-43.
The quality of data generated by high-throughput DNA sequencing tools must be rapidly assessed in order to determine how useful the datamay be in making biological discoveries; higher quality data leads to more confident results and conclusions. Due to the ever-increasing size of data sets and the importance of rapid quality assessment, tools that analyze sequencing data should quickly produce easily interpretable graphics. Quack addresses these issues by generating information-dense visualizations from FASTQ files at a speed far surpassing other publicly available quality assurance tools in a manner independent of sequencing technology.
Edrees A, Abdelhamed H, Nho SW, Park SB, Karsi A, Austin FW, Essa M, Pechan T, Lawrence ML (2018) Construction and evaluation of type III secretion system mutants of the catfish pathogen Edwardsiella piscicida. Journal of Fish Diseases 41(5): 805-816.
Catfish is the largest aquaculture industry in the United States. Edwardsiellosis is considered one of the most significant problems affecting this industry. Edwardsiella piscicida is a newly described species within the genus Edwardsiella, and it was previously classified as Edwardsiella tarda. It causes gastrointestinal septicaemia, primarily in summer months, in farmed channel catfish in the south-eastern United States. In the current study, we adapted gene deletion methods used for Edwardsiella to E. piscicida strain C07-087, which was isolated from a disease outbreak in a catfish production pond. Four genes encoding structural proteins in the type III secretion system (T3SS) apparatus of E. piscicida were deleted by homologous recombination and allelic exchange to produce in-frame deletion mutants (EpΔssaV, EpΔesaM, EpΔyscR and EpΔescT). The mutants were phenotypically characterized, and virulence and vaccine efficacy were evaluated. Three of the mutants, EpΔssaV, EpΔyscR and EpΔesaM, were significantly attenuated compared to the parent strain (p < .05), but EpΔescT strain was not. Vaccination of catfish with the four mutant strains (EpΔssaV, EpΔesaM, EpΔyscR and EpΔescT) provided significant protection when subsequently challenged with wild-type strain. In conclusion, we report methods for gene deletion in E. piscicida and development of vaccine candidates derived from a virulent catfish isolate.
Abdelhamed H, Ozdemir O, Tekedar HC, Arick MA 2nd, Hsu CY, Karsi A, Lawrence ML (2018) Complete Genome Sequence of Multidrug-Resistant Plesiomonas shigelloides Strain MS-17-188. Genome Announcements 6(18): e00387-18.
Plesiomonas shigelloides is a Gram-negative bacterium isolated from diverse environments. Here, we describe the complete genomesequence of the multidrug-resistant P. shigelloides strain MS-17-188, isolated from a diseased catfish. Availability of this genome will be beneficial for characterizing the molecular mechanisms of antibiotic resistance in this strain.
Wright AA, Sasidharan R, Koski L, Rodriguez-Carres M, Peterson DG, Nandula VK, Ray JD, Bond JA, Shaw DR (2018) Multiple Herbicide-Resistant Junglerice (Echinochloa colona): Identification of Genes Potentially Involved in Resistance through Differential Gene Expression Analysis. Weed Science 66: 347-354.
Herbicide resistance, and in particular multiple-herbicide resistance, poses an ever-increasing threat to food security. A biotype of junglerice [Echinochloa colona (L.) Link] with resistance to four herbicides, imazamox, fenoxaprop-P-ethyl, quinclorac, and propanil, each representing a different mechanism of action, was identified in Sunflower County, MS. Dose responses were performed on the resistant biotype and a biotype sensitive to all four herbicides to determine the level of resistance. Application of a cytochrome P450 inhibitor, malathion, with the herbicides imazamox and quinclorac resulted in increased susceptibility in the resistant biotype. Differential gene expression analysis of resistant and sensitive plants revealed that 170 transcripts were upregulated in resistant plants relative to sensitive plants and 160 transcripts were upregulated in sensitive plants. In addition, 507 transcripts were only expressed in resistant plants and 562 only in sensitive plants. A subset of these transcripts were investigated further using quantitative PCR (qPCR) to compare gene expression in resistant plants with expression in additional sensitive biotypes. The qPCR analysis identified two transcripts, a kinase and a glutathione S-transferase that were significantly upregulated in resistant plants compared with the sensitive plants. A third transcript, encoding an F-box protein, was downregulated in the resistant plants relative to the sensitive plants. As no cytochrome P450s were differentially expressed between the resistant and sensitive plants, a single-nucleotide polymorphism analysis was performed, revealing several nonsynonymous point mutations of interest. These candidate genes will require further study to elucidate the resistance mechanisms present in the resistant biotype.