Abdelhamed H, Ozdemir O, Ibrahim I, Lawrence M, Karsi A (2019) Antibacterial activities of trans-cinnamaldehyde, caprylic acid, and β-resorcylic acid against catfish pathogens. Aquaculture 504: 334-344.
Bacterial pathogens such as Edwardsiella ictaluri, Flavobacterium columnare, and virulent Aeromonas hydrophila have a significant economic impact on farm-raised catfish in the United States. Due to the limited number of licensed vaccines, and regulations with antimicrobials usage, there is need to find alternative therapeutics for sustainable aquaculture. Therefore, the antibacterial activities of trans-cinnamaldehyde (TC), caprylic acid (CA), and β-resorcylic acid (BA) were assessed against E. ictaluri 93–146, F. columnare 94–081, and A. hydrophila ML09–119 using broth microdilutions, and the capacity of TC to prevent E. ictaluri infection was evaluated during a challenge trial. Results demonstrated that TC inhibited growth of E. ictaluri, F. columnare, and A. hydrophila at 40, 20, and 80 µg/ml. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) of E. ictaluri, F. columnare, and A. hydrophila after incubation with TC revealed cell wall lysis, leakage of cytoplasmic contents, and pleomorphism in the bacterial shape with rupture of outer membranes. By the histological analysis, no abnormal changes were observed in the catfish intestines as a result of supplementation of TC. Moreover, an increasing number of goblet cells was observed in catfish received TC compared to control. In the E. ictaluri challenge trial, significantly higher survival was found in catfish that received TC at the levels of 15 and 20 mg/kg compared to control group (49.12% and 65.52% survival vs 11.11% survival). Bacterial concentrations in spleen and anterior kidney were significantly (P <.05) lower in fish fed with TC (20 mg/kg diet) compared to control at 5-day post-infection. Results indicate that supplementation of catfish feed with TC reduces E. ictaluri infection. A safe and efficacious alternative to antimicrobials will reduce the emergence and spread of antimicrobial resistant strains.
Omer AR, Henderson JE, Falconer L, Kroger R, Allen PJ (2019) Economic costs of using tailwater recovery systems for maintaining water quality and irrigation. Journal of Environmental Management 235: 186-193.
Best management practices (BMPs) are conservation efforts implemented to address environmental challenges associated with agricultural production. One such BMP, a tailwater recovery (TWR) system, has a dual purpose aimed at mitigating solids and nutrient losses from agricultural landscapes and creating an additional surface water source for irrigation. This study analyzes the costs of using five TWR systems to reduce solids, nutrients, and retain water. All systems were located in the Lower Mississippi Alluvial Valley and were used to irrigate crops including rice (Oryza sativa), corn (Zea mays), and soybeans (Glycine max). Costs to reduce solids and nutrients were calculated using annual payments and revenue losses due to lost tillable area from implementation of TWR systems. Similarly, cost to save and irrigate a mega-liter (ML) of water was determined as the annual payment for TWR systems, revenue losses and measured pumping cost. The range of mean total cost to reduce solids using TWR systems was $0 to $0.77 per kg; P was $0.61 to $3315.72 per kg; and N was $0.13 to $396.44 per kg. The range of mean total cost to retain water using TWR systems was $189.73 to $628.23 per ML, compared to a range of mean cost of groundwater of $13.99 to $36.17 per ML. Compared to other BMPs, TWR systems are one of the least expensive ways to reduce solid losses but remain an expensive way to reduce nutrient losses. The costs of using TWR systems to provide an additional irrigation water source range from less expensive than common conservation practices used to improve water use efficiency to more expensive and comparable to practices such as desalination. Therefore, TWR systems may be a prohibitively more expensive BMP to retain nutrients and water on some agricultural landscapes than other solutions.
Cai L, Jeremic D, Lim H, Kim Y (2019) β-Cyclodextrins as sustained-release carriers for natural wood preservatives. Industrial Crops and Products 130: 42-48.
Natural preservatives for wood protection have gained increasing attention due to their intrinsic antimicrobial properties, renewability, and lower impact on the environment. We report a study on the use of β-cyclodextrin (βCD) derivatives as sustained-release carriers of allyl isothiocyanate (AITC), as a model natural preservative compound. The formation of AITC inclusion complex in βCDs is qualitatively confirmed by FT-IR and the maximum inclusion yield is estimated to be 39%. Impregnation of wood with the water-borne βCD-AITC complexes allows penetration and even distribution of the preservative in the lumen and possibly in the cell walls. The efficacy of the βCD-AITC complexes as wood preservatives of southern yellow pine is examined by the AWPA E10-16 standard. Compared with the water-treated and AITC-treated wood, βCD-AITC-treated wood exhibits decrease in mass loss from 45% to 25% and no visible cell wall damage after exposure to brown and white rot fungi. The results indicate that βCD suppresses the premature leaching of otherwise volatile AITC and suggests a novel approach of application of volatile or water-immiscible natural preservatives for wood protection.
Abdelhamed H, Lawrence ML, Waldbieser G (2019) Complete genome sequence data of multidrug-resistant Aeromonas veronii strain MS-18-37. Data in Brief 23: 103689.
Aeromonas are Gram-negative, non-spore forming rods belonging to the family Aeromonadaceae within the class Gammaproteobacteria. These facultative anaerobic bacteria are ubiquitous in aquatic environments and have a broad host range. We present here the complete genome sequence of multidrug-resistant A. veronii strain MS-18-37 isolated from diseased catfish. The genome size of this strain is 4,683,931, with a G+C content of 58.60%. Annotation reveals multiple genes that encode antibiotic resistance. The complete genome sequence of A. veronii strain MS-18-37 will provide a genetic basis for understanding molecular mechanisms of antimicrobial resistance and exchange in Aeromonas.
Gastal GDA, Aguiar FLN, Ishak GM, Cavinder CA, Willard ST, Ryan PL, Feugang JM, Gastal EL (2019) Effect of cryopreservation techniques on proliferation and apoptosis of cultured equine ovarian tissue. Theriogenology 126: 88-94.
Preservation of cellular integrity and its mechanisms after ovarian tissue cryopreservation (OTC) and in vitro culture (IVC) procedures are crucial aspects for the success of preservation and recovery of female fertility. This study aimed to evaluate the effects of two cryopreservation methods (slow-freezing, SF, and vitrification, VIT) on the equine ovarian tissue after 1, 3, and 7 days of IVC by assessing: (i) preantral follicle morphology and distribution of follicle classes; (ii) protein expression of markers of cell proliferation for EGFR and Ki-67; (iii) markers of apoptosis for Bax and Bcl-2; and (iv) DNA fragmentation. Percentages of normal primordial follicles were similar (P > 0.05) among SF-control, VIT-control, and fresh control groups. After 7 days of culture, VIT-IVC7 had a greater (P < 0.05) total percentage of normal preantral follicles when compared with SF-IVC7, but both had a lower (P < 0.05) percentage than fresh IVC7 group. Prior to and after 7 days of culture, expression of EGFR and Ki-67 were similar (P > 0.05) among fresh, SF, and VIT groups. After 7 days of culture, VIT had higher (P < 0.05) Bax expression than the fresh and SF tissues, but Bcl-2 was similar (P > 0.05) among groups. Prior to IVC, TUNEL signals were similar (P > 0.05) among groups; however, VIT-IVC7 had greater (P < 0.05) TUNEL signals when compared with the fresh IVC7 group. In conclusion, findings demonstrated: (i) similar efficiency between SF and VIT compared with fresh control to preserve morphologically normal follicles; and (ii) similar tissue functionality and cell proliferation capability after equine OTC by either SF and VIT methods following IVC for 7 days. The results herein presented shed light on equine fertility preservation programs using OTC techniques.
Durfey CL, Swistek SE, Liao SF, Crenshaw MA, Clemente HJ, Thirumalai RVKG, Steadman CS, Ryan PL, Willard ST, Feugang JM (2019) Nanotechnology-based approach for safer enrichment of semen with best spermatozoa. Journal of Animal Science and Biotechnology 10(1): 14.
Background: Advances in nanotechnology have permitted molecular-based targeting of cells through safe and biocompatible magnetic nanoparticles (MNP). Their use to detect and remove damaged spermatozoa from semen doses could be of great interest. Here, MNP were synthesized and tested for their ability to target apoptotic (annexin V) and acrosome-reacted (lectin) boar spermatozoa, for high-throughout retrieval in a magnetic field (nanoselection). The potential impacts of nanoselection on sperm functions and performance of offspring sired by sperm subjected to nanoselection were determined. Fresh harvested and extended boar semen was mixed with various amounts (0, 87.5, and 175 µg) of MNP-conjugates (Annexin V-MNP or Lectin-MNP) and incubated (10 to 15 min) for 37 °C in Exp. 1. In Exp. 2, extended semen was mixed with optimal concentrations of MNP-conjugates and incubated (0, 30, 90, or 120 min). In Exp. 3, the synergistic effects of both MNP-conjugates (87.5 µg - 30 min) on spermatozoa was evaluated, followed by sperm fertility assessments through pregnancy of inseminated gilts and performance of neonatal offspring. Sperm motion, viability, and morphology characteristics were evaluated in all experiments. Results: Transmission electron microscopy, atomic force microscopy, and hyperspectral imaging techniques were used to confirm attachment of MNP-conjugates to damaged spermatozoa. The motility of nanoselected spermatozoa was improved (P < 0.05). The viability of boar sperm, as assessed by the abundance of reactive oxygen species and the integrity of the acrosome, plasma membrane, and mitochondrial membrane was not different between nanoselected and control spermatozoa. The fertility of gilts inseminated with control or nanoselected spermatozoa, as well as growth and health of their offspring were not different between (P > 0.05). Conclusions: The findings revealed the benefit of magnetic nanoselection for high-throughput targeting of damaged sperm, for removal and rapid and effortless enrichment of semen doses with highly motile, viable, and fertile spermatozoa. Therefore, magnetic nanoselection for removal of abnormal spermatozoa from semen is a promising tool for improving fertility of males, particularly during periods, such as heat stress during the summer months.
De Abrew Abeysundara P, Dhowlaghar N, Nannapaneni R (2019) Influence of cold stress on the survival of Listeria monocytogenes Bug600 and ScottA in lethal alkali, acid and oxidative stress. LWT - Food Science and Technology 100: 40-47.
The objective of this study was to determine the influence of cold stress (4 °C) on the survival of Listeria monocytogenes Bug600 and ScottA in lethal alkali, acid and oxidative stress in broth and in distilled water. Four distinct patterns were observed: (1) Survival of cold stressed L. monocytogenes was increased by 1–4 logs in lethal alkali stress (pH 12.3 NaOH or KOH); (2) Survival of cold stressed L. monocytogenes was decreased by 1–4 logs in lethal acid stress (pH 1.3 HCl or H3PO4); (3) Survival of cold stressed L. monocytogenes was increased by 1–4 logs in lethal oxidative stress (1500 ppm H2O2); and (4) No difference in survival of cold stressed L. monocytogenes was observed in lethal oxidative stress by chlorine (1000 ppm NaOCl) compared to control. These patterns were also consistently observed for survival of L. monocytogenes cells in lethal alkali, acid or oxidative stress after adaptation of cold stress at 4 °C in low nutrient conditions (1/10 TSBYE). These findings demonstrate that cold stressed cells of L. monocytogenes Bug600 and ScottA have greater tolerance to lethal alkali and some oxidative stresses that are commonly employed by the food industries to kill this foodborne pathogen.
You W, Yang Z, Guo G, Wan XF, Ji G (2018) Prediction of DNA-binding proteins by interaction fusion feature representation and selective ensemble. Knowledge-Based Systems 163: 598-610.
DNA-binding proteins play important roles in various cellular processes, and the identification of DNA-binding proteins is important for understanding and interpreting protein function. This manuscript presents algorithms for feature representation based on primary protein sequences and selective ensemble classification. We first propose a multi-source interaction fusion feature representation model that simultaneously considers interactions among physicochemical properties, evolutionary information, and gap distances between residues. We also provide a selective ensemble algorithm based on gap distances that yields differential base classifiers by selecting the feature subspaces. The selective ensemble algorithm improves the generalization ability of the integrated classifiers. We then compare the proposed algorithms with some state-of-the-art methods using multiple datasets. The experimental results show that the proposed algorithms are competitive and effectively identify DNA-binding proteins. The major contributions of the present study are the establishment of a model and algorithm for feature representation that involves interaction efforts and the development of a selective ensemble classification algorithm based on parameter perturbation. The proposed algorithms can also be applied to other biological questions related to amino acid sequences.
Takac T, Samajova O, Vadovic P, Pechan T, Samaj J (2019) Shot-gun proteomic analysis on roots of arabidopsis pldα1 mutants suggesting the involvement of PLDα1 in mitochondrial protein import, vesicular trafficking and glucosinolate biosynthesis. International Journal of Molecular Sciences 20(1): 82.
Phospholipase Dα1 (PLDα1) belongs to phospholipases, a large phospholipid hydrolyzing protein family. PLDα1 has a substrate preference for phosphatidylcholine leading to enzymatic production of phosphatidic acid, a lipid second messenger with multiple cellular functions. PLDα1 itself is implicated in biotic and abiotic stress responses. Here, we present a shot-gun differential proteomic analysis on roots of two Arabidopsis pldα1 mutants compared to the wild type. Interestingly, PLDα1 deficiency leads to altered abundances of proteins involved in diverse processes related to membrane transport including endocytosis and endoplasmic reticulum-Golgi transport. PLDα1 may be involved in the stability of attachment sites of endoplasmic reticulum to the plasma membrane as suggested by increased abundance of synaptotagmin 1, which was validated by immunoblotting and whole-mount immunolabelling analyses. Moreover, we noticed a robust abundance alterations of proteins involved in mitochondrial import and electron transport chain. Notably, the abundances of numerous proteins implicated in glucosinolate biosynthesis were also affected in pldα1 mutants. Our results suggest a broader biological involvement of PLDα1 than anticipated thus far, especially in the processes such as endomembrane transport, mitochondrial protein import and protein quality control, as well as glucosinolate biosynthesis.
Schuler GA, Brown MW (2019) Description of Armaparvus languidus n. gen. n. sp. Confirms Ultrastructural Unity of Cutosea (Amoebozoa, Evosea). Journal of Eukaryotic Microbiology 66(1): 158-166.
The American Type Culture Collection (ATCC) PRA-29 isolate has a publicly available transcriptome, which has led to its inclusion in recent phylogenomic analyses. The ATCC PRA-29 isolate was originally identified and deposited as “Pessonella sp.” This taxon branches robustly within the recently discovered clade Cutosea, very distantly related to the clade in which the genus Pessonella is believed to branch based on morphological data. Using detailed light and electron microscopy, we studied the morphology and ultrastructure of ATCC PRA-29 as well as other cutosean amoebae to better elucidate the morphological affinity of ATCC PRA-29 to other amoebozoans. Here, we show that ATCC PRA-29 was misidentified by the original depositor as Pessonella and name it Armaparvus languidus n. gen. n. sp. We show that a cell coat of microscales separated from the cell membrane is a unique trait found in all known cutosean amoebae. As Cutosea represents a clade at the deepest bifurcation in the amoebozoan group Evosea and because this clade is currently taxon-poor, but likely represents a major understudied group it will be important to isolate and describe more cutosean amoebae in the future.
Ravichandran A, Geng M, Hull KG, Li J, Romo D, Lu S-E, Albee A, Nutter C, Gordon DM, Ghannoum MA, Lockless SW, Smith L (2019) A novel actin binding drug with in vivo efficacy. Antimicrobial Agents and Chemotherapy 63(1): e01585-18.
Occidiofungin is produced by the soil bacterium Burkolderia contaminans MS14 and is structurally similar or identical to the burkholdines, xylocandins, and cepacidines. This study identified the primary cellular target of occidiofungin, which was determined to be actin. The modification of occidiofungin with a functional alkyne group enabled affinity purification assays and localization studies in yeast. Occidiofungin has a subtle effect on actin dynamics that triggers apoptotic cell death. We demonstrate the highly specific localization of occidiofungin to cellular regions rich in actin in yeast and the binding of occidiofungin to purified actin in vitro. Furthermore, a disruption of actin-mediated cellular processes, such as endocytosis, nuclear segregation, and hyphal formation, was observed. All of these processes require the formation of stable actin cables, which are disrupted following the addition of a subinhibitory concentration of occidiofungin. We were also able to demonstrate the effectiveness of occidiofungin in treating a vulvovaginal yeast infection in a murine model. The results of this study are important for the development of an efficacious novel class of actin binding drugs that may fill the existing gap in treatment options for fungal infections or different types of cancer.
Han L, Li L, Wen F, Zhong L, Zhang T, Wan X-F (2019) Graph-guided multi-task sparse learning model: a method for identifying antigenic variants of influenza A(H3N2) virus. Bioinformatics (Oxford, England) 35(1): 77-87.
Motivation: Influenza virus antigenic variants continue to emerge and cause disease outbreaks. Time-consuming, costly and middle-throughput serologic methods using virus isolates are routinely used to identify influenza antigenic variants for vaccine strain selection. However, the resulting data are notoriously noisy and difficult to interpret and integrate because of variations in reagents, supplies and protocol implementation. A novel method without such limitations is needed for antigenic variant identification. Results: We developed a Graph-Guided Multi-Task Sparse Learning (GG-MTSL) model that uses multi-sourced serologic data to learn antigenicity-associated mutations and infer antigenic variants. By applying GG-MTSL to influenza H3N2 hemagglutinin sequences, we showed the method enables rapid characterization of antigenic profiles and identification of antigenic variants in real time and on a large scale. Furthermore, sequences can be generated directly by using clinical samples, thus minimizing biases due to culture-adapted mutation during virus isolation. Availability and implementation: MATLAB source codes developed for GG-MTSL are available through http://sysbio.cvm.msstate.edu/files/GG-MTSL/. Supplementary information: Supplementary data are available at Bioinformatics online.
Grover CE, Arick-2nd MA, Thrash A, Conover JL, Sanders WS, Peterson DG, Frelichowski JE, Scheffler JA, Scheffler BE, Wendel JF (2019) Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing. Genome Biology and Evolution 11(1): 53-71.
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33× genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2-fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.
Glasa M, Predajna L, Wetzel T, Rheinpfalz DLR, Soltys K, Sabanadzovic S (2019) First report of grapevine rupestris vein feathering virus in grapevine in slovakia. Plant Disease 103(1): 170.
Dhakal J, Sharma CS, Nannapaneni R, McDaniel CD, Kim T, Kiess A (2019) Effect of chlorine-induced sublethal oxidative stress on the biofilm-forming ability of salmonella at different temperatures, nutrient conditions, and substrates. Journal of Food Protection 82(1): 78-92.
The present study was conducted to evaluate the effect of chlorine-induced oxidative stress on biofilm formation by various Salmonella strains on polystyrene and stainless steel (SS) surfaces at three temperatures (30, 25 [room temperature], and 4°C) in tryptic soy broth (TSB) and 1/10 TSB. Fifteen Salmonella strains (six serotypes) were exposed to a sublethal chlorine concentration (150 ppm of total chlorine) in TSB for 2 h at the predetermined temperatures. The biofilm-forming ability of the Salmonella strains was determined in 96-well polystyrene microtiter plates by using a crystal violet staining method and on SS coupons in 24-well tissue culture plates. All tested strains of Salmonella produced biofilms on both surfaces tested at room temperature and at 30°C. Of the 15 strains tested, none (chlorine stressed and nonstressed) formed biofilm at 4°C. At 30°C, Salmonella Heidelberg (ID 72), Salmonella Newport (ID 107), and Salmonella Typhimurium (ATCC 14028) formed more biofilm than did their respective nonstressed controls on polystyrene (P ≤ 0.05). At room temperature, only stressed Salmonella Reading (ID 115) in 1/10 TSB had significantly more biofilm formation than did the nonstressed control cells (P ≤ 0.05). Salmonella strains formed more biofilm in nutrient-deficient medium (1/10 TSB) than in full-strength TSB. At 25°C, chlorine-stressed Salmonella Heidelberg (ATCC 8326) and Salmonella Enteritidis (ATCC 4931) formed stronger biofilms on SS coupons (P ≤ 0.05) than did the nonstressed cells. These findings suggest that certain strains of Salmonella can produce significantly stronger biofilms on plastic and SS upon exposure to sublethal chlorine.