Interstate 80 Lakes — Grand Island to Elm Creek Fish Survey Results - Spring 2013

Spanning a stretch of 150 miles along Interstate 80 from Grand Island to Hershey more than 60 small lakes are available for public fishing. Fisheries staff from the Kearney office has the management responsibility for the Interstate lakes located from Grand Island to Elm Creek. These man-made lakes, most of which were created for fill material when the Interstate system was developed in the 1960’s, range in size from 1 to 42 acres. The ground water fed lakes have excellent shoreline access for anglers and usually contain clear water and abundant aquatic vegetation, providing excellent habitat conditions for largemouth bass and bluegill. In addition, most of the lakes contain channel catfish, while others have crappie, rock bass, walleye, and northern pike. The fish populations are surveyed on a five year rotation and the following graphs and text display these results. Largemouth Bass Largemouth bass are present in all of the Interstate lakes in the central portion of Nebraska, with the exception of War Axe, which has smallmouth bass. Lakes with high densities of smaller bass, include Windmill, Ft. Kearny, West and Middle Mormon Island, Bufflehead, Kea Lake, Coot Shallows, and Sandy Channel #2. Lakes that traditionally produce large bass include Cheyenne, Windmill #1, Bassway Strip, Bufflehead, Blue Hole West, and Sandy Channel #8. Most of the I-80 lakes have a 15-inch minimum length limit on black bass. Exceptions include; Mormon Island SRA, Cheyenne, West Wood River, War Axe, and Archway Lakes, all of which have a 21-inch minimum length limit. In addition, Kea West is designated as a catch and release only lake for all species. Anglers are encouraged to practice catch and release on bass in the I-80 Lakes as they are easily over-harvested

Niobrara-Missouri River Fishery Investigations

The Niobrara River heads in the table lands of eastern Wyoming and flows 786 kilometers (km) eastward across Nebraska joining the Missouri River near the town of Niobrara, Nebraska. The Niobrara is the largest Missouri River tributary between the last two mainstem impoundments (Lake Francis Case and Lewis and Clark Lake). Fish movement up the Niobrara is prevented by Nebraska Public Power District\u27s (NPPD\u27s) Spencer Hydroelectric Dam, 63.3 km upstream from the river mouth. The lower reach of the river is turbid and carries a considerable load of sand, silt, and organic debris into the Missouri River. The mean annual flow is 49.5 m3/s. The mean annual flow through Spencer Dam for the period September 1976 through September 1977 was 37.7 m3/s. Silt, sand, and debris settle into the reservoir behind Spencer Dam. Periodic flushing is needed to prevent damage to the turbines. Quarterly flushings have resulted in significant fish kills downstream from Spencer Dam (Hesse 1976, Hesse 1977, Wallace 1976). Niobrara River fish populations have not been studied previously. In contrast, the fishery of the Missouri River-L.ewis and Clark Lake system was studied by the U.S. Fish and Wildlife Service from 1962- 1974 (Walburg 1976). Walburg alluded to the beneficial relationship that potentially exists between the Niobrara and Missouri river systems. The fishery in Lewis and Clark Lake has been declining since 1959 for reasons that are well defined (Walburg 1964, Walburg 1976). The Niobrara is a major tributary and may offer a better spawning and nursery environment than the Missouri-Lewis and Clark system. This study was designed to distinguish the relationship existing between the fisheries of these two systems and establish a baseline of life history data for Niobrara fishes for future reference. This information is especially valuable, since proposals by the U.S. Bureau of Reclamation would create an impoundment on the Niobrara (O\u27Neill-Norden Dam Irrigation Project) approximately 208 km upstream from the mouth of the river. Should this project become reality, flows in the Niobrara at Norden, Nebraska, would be reduced from the 21.9 m3/s mean annual flow for the period 1964-73 (Nebraska Natural Resources Commission 1976). Projected flow through Norden Dam would be 5.7 m3/s for 60% of the time {personal communication with Roger Andrews, U.S. Bureau of Reclamation). Reduced flow will surely restrict fisheries habitat in the lower Niobrara. If the Niobrara River is a significant contributor to the fishery of the Missouri River - Lewis and Clark Lake system, a loss of fish habitat in the Niobrara could have a detrimental effect on the fishery of the larger system. Collection of data at this time will aid in the assessment of such losses if they occur

Landscape of somatic single nucleotide variants and indels in colorectal cancer and impact on survival

Colorectal cancer (CRC) is a biologically heterogeneous disease. To characterize its mutational profile, we conduct targeted sequencing of 205 genes for 2,105 CRC cases with survival data. Our data shows several findings in addition to enhancing the existing knowledge of CRC. We identify PRKCI, SPZ1, MUTYH, MAP2K4, FETUB, and TGFBR2 as additional genes significantly mutated in CRC. We find that among hypermutated tumors, an increased mutation burden is associated with improved CRC-specific survival (HR=0.42, 95% CI: 0.21-0.82). Mutations in TP53 are associated with poorer CRC-specific survival, which is most pronounced in cases carrying TP53 mutations with predicted 0% transcriptional activity (HR=1.53, 95% CI: 1.21-1.94). Furthermore, we observe differences in mutational frequency of several genes and pathways by tumor location, stage, and sex. Overall, this large study provides deep insights into somatic mutations in CRC, and their potential relationships with survival and tumor features. Large scale sequencing study is of paramount importance to unravel the heterogeneity of colorectal cancer. Here, the authors sequenced 205 cancer genes in more than 2000 tumours and identified additional mutated driver genes, determined that mutational burden and specific mutations in TP53 are associated with survival odds

A Case Study of a Successful Lake Rehabilitation Project in South-Central Nebraska

Cottonmill Lake, a 17.4 ha impoundment located in Buffalo County, Nebraska, was a fishery dominated by common carp (Cyprinus carpio). As a result of the poor sportfish populations, angler participation in May and June of 1993 was low (503 ± 210 angler hours) and angler catch rates for all fish species (0.5 ± 0.4 fish/angler hour) was less than desired. In 1995, before rehabilitation, bluegill (Lepomis macrochirus) trap net catch per unit effort (CPUE) was 1.5 ± 0.9, largemouth bass (Micropterus salmoides) catch per hour of electrofishing was 8.0 ± 0.5, and channel catfish (Ictalurus punctatus) CPUE in gill nets was 7.5 ± 2.5. In 1999, the Nebraska Game and Parks Commission (NGPC) and city of Kearney completed a lake rehabilitation project at Cottonmill Lake by removing 84,995 m3 (300,000 ft3) of sediment and adding two islands and four breakwater jetties. Standardized NGPC fishery survey conducted in 2003, four years after rehabilitation, found a significant increase in number of bluegill (CPUE = 28.3 ± 7.4; p = 0.012; F = 12.86; df= 1) and largemouth bass (CPUE = 496.0 ± 5.8; p \u3c 0.001; F = 34.33; df= 1). In addition, angler participation in May and June 2006 was higher after rehabilitation (11,122 ± 1,333 angler hours), and angler catch rates for all species (1.5 ± 0.4 fish/angler hour) increased. The estimated angler expenditure while fishing at Cottonmill Lake during May and June 2006 increased to $367,026 in 2006 from an estimated$26,004 during May and June 1993

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu