Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

The high‐throughput capacities of the Illumina sequencing platforms and the possibility to label samples individually have encouraged wide use of sample multiplexing. However, this practice results in read misassignment (usually <1%) across samples sequenced on the same lane. Alarmingly high rates of read misassignment of up to 10% were reported for lllumina sequencing machines with exclusion amplification chemistry. This may make use of these platforms prohibitive, particularly in studies that rely on low‐quantity and low‐quality samples, such as historical and archaeological specimens. Here, we use barcodes, short sequences that are ligated to both ends of the DNA insert, to directly quantify the rate of index hopping in 100‐year old museum‐preserved gorilla (Gorilla beringei) samples. Correcting for multiple sources of noise, we identify on average 0.470% of reads containing a hopped index. We show that sample‐specific quantity of misassigned reads depends on the number of reads that any given sample contributes to the total sequencing pool, so that samples with few sequenced reads receive the greatest proportion of misassigned reads. This particularly affects ancient DNA samples, as these frequently differ in their DNA quantity and endogenous content. Through simulations we show that even low rates of index hopping, as reported here, can lead to biases in ancient DNA studies when multiplexing samples with vastly different quantities of endogenous material.     

基于多源数据的福州市中心城区人居环境质量评价

城市内部居住环境的客观性评价有助于发现城市发展中暴露出的问题,有针对性地进行调整进而改善城市环境。以福州市中心城区为研究区,居住区为研究单元,利用气象监测数据、遥感影像数据、地图兴趣点数据、国土规划数据等多源数据,从环境健康舒适性、交通便捷性、城市安全性和生活方便性4方面构建城市人居环境监测体系,并使用优劣解距离法进行人居环境质量综合评价。结果表明: 福州市中心城区人居环境水平差异性较大,整体上呈现出中心区域高、边缘地区低的特点。城区中部人居环境指数较高,东部和南部区域较低,西部和北部区域人居环境高值与低值混杂分布。各指标层中,交通便捷性和生活方便性的高-高集聚以及低-低集聚特征与人居环境高低值聚类分布较为一致,便捷的交通以及完备的服务设施对人居环境评价的影响较大;环境健康舒适性呈现城市内部低、边缘高的特点,而城市安全性呈现内部高、边缘低的特点。     

Assessing the Environmental Impact of Water Consumption by Energy Crops Grown in Spain

The environmental impact of the water consumption of four typical crop rotations grown in Spain, including energy crops, was analyzed and compared against Spanish agricultural and natural reference situations. The life cycle assessment (LCA) methodology was used for the assessment of the potential environmental impact of blue water (withdrawal from water bodies) and green water (uptake of soil moisture) consumption. The latter has so far been disregarded in LCA. To account for green water, two approaches have been applied: the first accounts for the difference in green water demand of the crops and a reference situation. The second is a green water scarcity index, which measures the fraction of the soil‐water plant consumption to the available green water. Our results show that, if the aim is to minimize the environmental impacts of water consumption, the energy crop rotations assessed in this study were most suitable in basins in the northeast of Spain. In contrast, the energy crops grown in basins in the southeast of Spain were associated with the greatest environmental impacts. Further research into the integration of quantitative green water assessment in LCA is crucial in studies of systems with a high dependence on green water resources.     

Diatoms as indicators: The influences of experimental nitrogen enrichment on diatom assemblages in sub-Arctic streams

Indices using diatoms are widely used to assess water quality, but are usually constructed from field correlations and not tested through rigorous experimentation. We tested experimentally the performance of the Sørensen and the Shannon indices, and the trophic diatom index (TDI). Nitrogen was naturally limiting in the eight remote sub-Arctic streams used and we measured the effects of experimental nitrogen enrichment on diatom assemblages. Diatom densities increased significantly in the enriched reaches but there was no significant difference in invertebrate density between control and treatment reaches. Grazing effects were thus controlled for. Diversity within streams (Shannon index) was significantly reduced by nutrient addition but the Sørensen index did not change. The trophic diatom index (TDI), which is presumed to reflect nutrient concentration, was not influenced by nutrient addition and generally the values were low in both control and treatment reaches. Densities of the diatom genera Achnanthes and Gomphonema increased significantly with enrichment while those of Nitzschia and Fragilaria decreased significantly. Less abundant diatom species, which collectively constituted around 40% in relative abundance in the control reaches, were around 15–18% in treatment reaches. Growth forms were altered by the nutrients. Diatoms attached by mucilage pads were more abundant in treated reaches compared with control reaches. Motile diatoms became scarcer. The size of diatom species was unaffected by nutrient enrichment. This study showed that it is important to test experimentally indices that are developed for particular habitats before using them elsewhere.     

Difference in Ki67 and Thymidylate Synthase Expression in Primary Tumour Compared with Metastatic Nodes in Breast Cancer Patients

Breast cancer is a heterogeneous disease, so therapeutic predictive biological markers need to be identified. To date an accurate evaluation of predictive markers is mainly done at the primary site; however, the main goal of adjuvant therapy for breast cancer is the control of micrometastases. The aim of this study is to assess as therapeutic and/or prognostic marker, the proliferation status of primary tumors and involved nodes as measured by Ki67 and thymidylate synthase (TS) expression, in 30 breast cancer node positive patients. TS is the main target of 5-fluorouracil (5-FU) activity, and its overexpression is one of the mechanisms of 5-FU drug resistance; however, in some studies its absence is responsible for a worse response to 5-FU. Our results show that malignant cells of involved nodes were in a post mitotic phase of the cell cycle, and show a low proliferation index and TS expression, while the primary tumours and controls, were strongly positive. On these basis we can hypothesize that these cells could be less sensitive to 5-FU. Further studies are necessary to identify other mechanisms responsible for their metastasing capability and/or for their aggressiveness.     

Feeding dynamics of Palaemon peringueyi (Decapoda,Caridea) in the temporarily open/closed Kasouga Estuary,South Africa

The feeding ecology of the caridean shrimp Palaemon peringueyi in the temporarily open/closed Kasouga Estuary, Eastern Cape, was examined during summer and winter employing stomach fullness index (SFI) analysis. Mean SFI values for male and female shrimp during summer ranged from 0.85% to 2.36% and from 0.56% and 2.61% body dry weight, respectively. During winter, SFI values for males and females were lower, and varied between 0.23% and 1.56% and 0.36% and 1.84% body dry weight, respectively. There were no significant differences in the SFI values between males and females during the two seasons. A peak in the feeding activity for both sexes was observed during the daytime during both summer and winter. For both males and females, non-linear regression analysis best explained the change in SFI over time. The gut evacuation rate constants (k) of males and females during summer were estimated at 0.43 h^?1 and 0.30 h^?1, respectively. These values correspond to a daily food intake equivalent to 16.2% body dwt for males and 11.1% body dwt for females. During winter, the gut evacuation rates of the shrimp were estimated at 0.35 h^?1 for males and 0.28 h^?1 for females. The daily ration for adult male and female shrimp during winter was estimated at 6.1% and 6.8% body dwt, respectively. The lower estimates obtained during winter appear largely to reflect the influence of the reduced water temperatures on the metabolic activities of the shrimp.     

Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae

The plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial blight, which is one of the most serious diseases of rice. Xoo has been studied for over one century, and much has been learned about it, but proteomic investigation has been neglected. In this study, proteome reference maps of Xoo were constructed by two-dimensional gel electrophoresis, and 628 spots in the gels representing 469 different protein species were identified with MALDI-TOF/TOF MS. The identified spots were assigned to 15 functional categories according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the annotations from the National Center for Biotechnology Information (NCBI) database. The data set has been deposited in the World-2DPAGE database (Database ID: 0044). In addition, comparative proteomic analysis revealed that proteins related to the TonB-dependent transportation system and energy metabolism are involved in the phenazine-1-carboxylic acid resistance in Xoo. In conclusion, we have established a proteome database for Xoo and have used this database in a comparative proteomic analysis that identified proteins potentially contributing to phenazine-1-carboxylic acid resistance in Xoo.     

Telocytes: new insight into the pathogenesis of gallstone disease

The major mechanisms of gallstone formation include biliary cholesterol hypersecretion, supersaturation and crystallization, mucus hypersecretion, gel formation and bile stasis. Gallbladder hypomotility seems to be a key event that triggers the precipitation of cholesterol microcrystals from supersaturated lithogenic bile. Telocytes, a new type of interstitial cells, have been recently identified in many organs, including gallbladder. Considering telocyte functions, it is presumed that these cells might be involved in the signalling processes. The purpose of this study was to correlate the quantity of telocytes in the gallbladder with the lithogenicity of bile. Gallbladder specimens were collected from 24 patients who underwent elective laparoscopic cholecystectomy for symptomatic gallstone disease. The control group consisted of 25 consecutive patients who received elective treatment for pancreatic head tumours. Telocytes were visualized in paraffin sections of gallbladders with double immunofluorescence using primary antibodies against c‐Kit (anti‐CD117) and anti‐mast cell tryptase. Cholesterol, phospholipid and bile acid levels were measured in gallbladder bile. The number of telocytes in the gallbladder wall was significantly lower in the study group than that in the control group (3.03 ± 1.43 versus 6.34 ± 1.66 cell/field of view in the muscularis propria, P < 0.001) and correlated with a significant increase in the cholesterol saturation index. The glycocholic and taurocholic acid levels were significantly elevated in the control subjects compared with the study group. The results suggest that bile composition may play an important role in the reduction in telocytes density in the gallbladder.     

The decline and rise of the Kransberg Cape Vulture colony over 35 years has implications for composite population indices and survey frequency

Long-term monitoring is key for detecting population declines. Composite indices allow researchers to combine trends from disparate monitoring programmes into a single estimate of population change. Inferences from composite indices, however, are limited to the time periods and areas studied. We show that the number of breeding pairs in a colony of Cape Vultures Gyps coprotheres in South Africa declined between the years 1983 and 2003 but increased in both the number of breeding pairs and fledglings per pair from 2004 to 2017. We performed a retrospective power analysis determining the minimum annual frequency with which the colony could have been monitored without sacrificing inference into population trends. This power analysis revealed the post-2003 population increase would not have been apparent if we skipped more than 2 years between surveys. We incorporated our estimates into a previously published composite index for Cape Vultures that considered only data collected pre-2000 and demonstrate that the inference is unchanged if the trend from the decline period or the entire study is incorporated, yet if only the trend during the period of population increase is used, there is no longer a statistically significant decline across the species’ range. Our results demonstrate the utility of long-term monitoring because if our study had concluded before 2003, there would be little evidence of the current population increase at Kransberg.     

Cloning and expression analysis of the cytochrome P450c17s enzymes during the reproductive cycle in ovoviviparous Korean rockfish (Sebastes schlegeli)

Cytochrome P450c17 (CYP17, 17α-hydroxylase/17, 20-lyase) plays a critical role in the production of androgens and estrogens in vertebrates. We isolated the full length cDNAs of P450c17-I and P450c17-II from Sebastes schlegeli. The cDNA sequences of P450c17-I and P450c17-II encoded 515 and 533 amino acid residues respectively. The putative P450c17-I and P450c17-II enzymes of Korean rockfish share high sequence identity with that of Japanese flounder (92% and 81%) respectively. Our current study describes that P450c17s of Korean rockfish are mainly expressed in gonads, head kidney and kidney by RT-PCR. Quantitative real-time PCR showed that the expression patterns of Korean rockfish P450c17s were developmental stage-dependency. In addition, the testosterone (T) and gonadosomatic index (GSI) levels further support the important role of P450c17-I during shift in steroidogenesis. Taken together, this study provides information about the Korean rockfish P450c17s characterization and mRNA expression as such helps in further understanding of its function in gonadal development.