Exploring Agricultural Production Systems and Their Fundamental Components with System Dynamics Modelling

Agricultural production in the United States is undergoing marked changes due to rapid shifts in consumer demands, input costs, and concerns for food safety and environmental impact. Agricultural production systems are comprised of multidimensional components and drivers that interact in complex ways to influence production sustainability. In a mixed-methods approach, we combine qualitative and quantitative data to develop and simulate a system dynamics model that explores the systemic interaction of these drivers on the economic, environmental and social sustainability of agricultural production. We then use this model to evaluate the role of each driver in determining the differences in sustainability between three distinct production systems: crops only, livestock only, and an integrated crops and livestock system. The result from these modelling efforts found that the greatest potential for sustainability existed with the crops only production system. While this study presents a stand-alone contribution to sector knowledge and practice, it encourages future research in this sector that employs similar systems-based methods to enable more sustainable practices and policies within agricultural production

Toadfish

24 p. : ill. ; 24 cm.Includes bibliographical references (p. 21-24)."Opsanus phobetron is described from the western Bahamas, Cuba, and the Isle of Pines. It was observed to nest in late December at Bimini, Bahamas. The black mouth functions as a warning mechanism, and under low albedo conditions, as at Bimini, the dark coloration is indicated to be of social significance. Attention is called to unidentified samples of Opsanus from Little Bahama Bank and the Gulf of Campeche. The ranges and recognition characters of O. pardus, O. tau, O. beta, and O. barbatus are discussed. Opsanus vandeuseni Fowler is referred to the synonymy of Opsanus beta (Goode and Bean). Opsanus hildebrandi Breder is placed in Marcgravia Jordan and appears not to be identical with M. ctyptocentra (Cuvier and Valenciennes). The low numbers of dorsal and anal rays attributed to Opsanus in the literature are valid if the Queensland genus Batrachoemus Ogilby is considered identical with Opsanus. Published paleotemperature measurements indicate that the 'tropical' Atlantic and Caribbean regions were not tropical during the last glacial period. The trans-Florida faunal province, now absent from southern Florida, was continuous around the southern tip of the Florida land mass; at the same time coral reefs were absent from most of the West Indies, and the shore fauna was predominantly temperate in the north and predominantly subtropical in the south. It is improbable that the Florida peninsula neck was submerged during Pleistocene interglacial periods. The presence of marine fishes in Florida fresh waters is not considered significant from the standpoint of historical zoogeography, and it is suggested that the elevated chlorinities in Florida fresh waters are maintained by current processes. Even if the neck of the Florida peninsula had been drowned, the Gulf of Mexico populations of trans-Florida fishes probably could not utilize the passage, as the temperatures would have been too high. The Gulf of Mexico disjunct trans-Florida populations are interpreted as glacial rather than interglacial relicts, and a comparison is drawn between the Gulf of Mexico and the Sea of Okhotsk. Because the spawning threshold temperature of Opsanus parallels the minimal thermal tolerance of reef corals, Opsanus is considered to be an 'indicator' of temperate coastal waters. Owing to thermal requirements and tolerances, Opsanus survives as a glacial relict in a few West Indian localities. During the last glacial period, the northern distributional limit for Opsanus may have been as far south as southern Florida. Opsanus, lacking pelagic life-history stages, could have dispersed through the West Indies by passive transport during storms"--P. 20-21

Fishes from Canada

17 p. ; 24 cm.Includes bibliographical references (p. 15-17)."The following fishes were collected: Alert: Salvelinus alpinus; Gymnelis virdis; Icelus bicornis; Myoxocephalus quadricornis; Liparis koefoedi; Liparis ? liparis. Mould Bay: Salvelinus alpinus; Boreogadus saida; Anarhichas denticulatus; Lycodes pallidus; Icelus bicornis; Myoxocephalus quadricornis; Eumicrotremus spinosus. 2. Two different forms of catfish are currently referred to Anarhichas denticulatus, but it is not known whether the differences are due to sex, age, or other factors, or whether or not the differences are specific. 3. The specimens of Icelus bicornis listed by Walters (1953) from various stations in Dolphin and Union Strait, Northwest Territories, probably consisted at least in part of Icelus spatula; one specimen may have been Icelus bicornis. 4. Cottus polaris Sabine (1821) and Porocottus polaris (Sabine) Jordan and Evermann are identical to Myoxocephalus quadricornis (Linnaeus). 5. Eumicrotremus pacificus Schmidt is not identical to E. orbis (Günther). 6. The record of Eumicrotremus birulai from the Kara Sea (Popov, 1933) should be regarded as probably E. spinosus. 7. Eumicrotremus spinosus variabilis Jensen (1944) is identical to E. derjugini Popov (1926)"--P. 14-15

MPLEx: a method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling

The continued emergence and spread of infectious agents is of great concern, and systems biology approaches to infectious disease research can advance our understanding of host–pathogen relationships and facilitate the development of new therapies and vaccines

A Regional Reduction in Ito and IKACh in the Murine Posterior Left Atrial Myocardium Is Associated with Action Potential Prolongation and Increased Ectopic Activity.

BACKGROUND: The left atrial posterior wall (LAPW) is potentially an important area for the development and maintenance of atrial fibrillation. We assessed whether there are regional electrical differences throughout the murine left atrial myocardium that could underlie regional differences in arrhythmia susceptibility. METHODS: We used high-resolution optical mapping and sharp microelectrode recordings to quantify regional differences in electrical activation and repolarisation within the intact, superfused murine left atrium and quantified regional ion channel mRNA expression by Taqman Low Density Array. We also performed selected cellular electrophysiology experiments to validate regional differences in ion channel function. RESULTS: Spontaneous ectopic activity was observed during sustained 1Hz pacing in 10/19 intact LA and this was abolished following resection of LAPW (0/19 resected LA, P<0.001). The source of the ectopic activity was the LAPW myocardium, distinct from the pulmonary vein sleeve and LAA, determined by optical mapping. Overall, LAPW action potentials (APs) were ca. 40% longer than the LAA and this region displayed more APD heterogeneity. mRNA expression of Kcna4, Kcnj3 and Kcnj5 was lower in the LAPW myocardium than in the LAA. Cardiomyocytes isolated from the LAPW had decreased Ito and a reduced IKACh current density at both positive and negative test potentials. CONCLUSIONS: The murine LAPW myocardium has a different electrical phenotype and ion channel mRNA expression profile compared with other regions of the LA, and this is associated with increased ectopic activity. If similar regional electrical differences are present in the human LA, then the LAPW may be a potential future target for treatment of atrial fibrillation

Analysis of SNPs and Haplotypes in Vitamin D Pathway Genes and Renal Cancer Risk

In the kidney vitamin D is converted to its active form. Since vitamin D exerts its activity through binding to the nuclear vitamin D receptor (VDR), most genetic studies have primarily focused on variation within this gene. Therefore, analysis of genetic variation in VDR and other vitamin D pathway genes may provide insight into the role of vitamin D in renal cell carcinoma (RCC) etiology. RCC cases (N = 777) and controls (N = 1,035) were genotyped to investigate the relationship between RCC risk and variation in eight target genes. Minimum-p-value permutation (Min-P) tests were used to identify genes associated with risk. A three single nucleotide polymorphism (SNP) sliding window was used to identify chromosomal regions with a False Discovery Rate of <10%, where subsequently, haplotype relative risks were computed in Haplostats. Min-P values showed that VDR (p-value = 0.02) and retinoid-X-receptor-alpha (RXRA) (p-value = 0.10) were associated with RCC risk. Within VDR, three haplotypes across two chromosomal regions of interest were identified. The first region, located within intron 2, contained two haplotypes that increased RCC risk by approximately 25%. The second region included a haplotype (rs2239179, rs12717991) across intron 4 that increased risk among participants with the TC (OR = 1.31, 95% CI = 1.09–1.57) haplotype compared to participants with the common haplotype, TT. Across RXRA, one haplotype located 3′ of the coding sequence (rs748964, rs3118523), increased RCC risk 35% among individuals with the variant haplotype compared to those with the most common haplotype. This study comprehensively evaluated genetic variation across eight vitamin D pathway genes in relation to RCC risk. We found increased risk associated with VDR and RXRA. Replication studies are warranted to confirm these findings

Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene

<p>Abstract</p> <p>Background</p> <p>The total number of miRNA genes in a genome, expression of which is responsible for the miRNA repertoire of an organism, is not precisely known. Moreover, the question of how new miRNA genes arise during evolution is incompletely understood. Recent data in humans and opossum indicate that retrotranspons of the class of short interspersed nuclear elements have contributed to the growth of microRNA gene clusters.</p> <p>Method</p> <p>We studied a large miRNA gene cluster in intron 10 of the mouse Sfmbt2 gene using bioinformatic tools.</p> <p>Results</p> <p>Mice and rats are unique to harbor a 55-65 Kb DNA sequence in intron 10 of the Sfmbt2 gene. This intronic region is rich in regularly repeated B1 retrotransposons together with inverted self-complementary CA/TG microsatellites. The smallest repeats unit, called MSHORT1 in the mouse, was duplicated 9 times in a tandem head-to-tail array to form 2.5 Kb MLONG1 units. The center of the mouse miRNA gene cluster consists of 13 copies of MLONG1. BLAST analysis of MSHORT1 in the mouse shows that the repeat unit is unique for intron 10 of the Sfmbt2 gene and suggest a dual phase model for growth of the miRNA gene cluster: arrangment of 10 MSHORT1 units into MLONG1 and further duplication of 13 head-to-tail MLONG1 units in the center of the miRNA gene cluster. Rats have a similar arrangment of repeat units in intron 10 of the Sfmbt2 gene. The discrepancy between 65 miRNA genes in the mouse cluster as compared to only 1 miRNA gene in the corresponding rat repeat cluster is ascribed to sequence differences between MSHORT1 and RSHORT1 that result in lateral-shifted, less-stable miRNA precursor hairpins for RSHORT1.</p> <p>Conclusion</p> <p>Our data provides new evidence for the emerging concept that lineage-specific retroposons have played an important role in the birth of new miRNA genes during evolution. The large difference in the number of miRNA genes in two closely related species (65 versus 1, mice versus rats) indicates that this species-specific evolution can be a rapid process.</p

Infantile Convulsions with Paroxysmal Dyskinesia (ICCA Syndrome) and Copy Number Variation at Human Chromosome 16p11

BACKGROUND: Benign infantile convulsions and paroxysmal dyskinesia are episodic cerebral disorders that can share common genetic bases. They can be co-inherited as one single autosomal dominant trait (ICCA syndrome); the disease ICCA gene maps at chromosome 16p12-q12. Despite intensive and conventional mutation screening, the ICCA gene remains unknown to date. The critical area displays highly complicated genomic architecture and is the site of deletions and duplications associated with various diseases. The possibility that the ICCA syndrome is related to the existence of large-scale genomic alterations was addressed in the present study. METHODOLOGY/PRINCIPAL FINDINGS: A combination of whole genome and dedicated oligonucleotide array comparative genomic hybridization coupled with quantitative polymerase chain reaction was used. Low copy number of a region corresponding to a genomic variant (Variation_7105) located at 16p11 nearby the centromere was detected with statistical significance at much higher frequency in patients from ICCA families than in ethnically matched controls. The genomic variant showed no apparent difference in size and copy number between patients and controls, making it very unlikely that the genomic alteration detected here is ICCA-specific. Furthermore, no other genomic alteration that would directly cause the ICCA syndrome in those nine families was detected in the ICCA critical area. CONCLUSIONS/SIGNIFICANCE: Our data excluded that inherited genomic deletion or duplication events directly cause the ICCA syndrome; rather, they help narrowing down the critical ICCA region dramatically and indicate that the disease ICCA genetic defect lies very close to or within Variation_7105 and hence should now be searched in the corresponding genomic area and its surrounding regions