Transcriptomic analyses of regenerating adult feathers in chicken

Transcriptome Expression Data. Table of mapped reads to Galgal4 transcripts for all 15 data sets. FPKM (Fragments per kilobase of exon per million fragments mapped): normalized transcript abundance values for each gene in the indicated tissues. (CSV 1314 kb

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

A Genetic Analysis of Pedigree and Egg Production for the Conserved Populations of Taiwan Country Chicken

維持遺傳多樣性是保種主要的議題。豐富的遺傳資源對家畜禽的發展與改良是一個重要的關鍵，因此族群保存必須同時維持遺傳的多樣性。近親係數是品種保存的重要訊息，但其計算非常倚賴系譜的資訊。一個長期維持的族群，可能因疏於管理導致資料遺失或是配種策略改變，使近親係數的估計產生偏差甚至無法計算。地方雞種因生產性能不佳，在外來高效益商業品種的壓力下，已有滅種的危機，有品種保存之必要，但以小族群保存可能會因近親配種而產生近親衰退及遺傳多樣性喪失的現象。本研究分為兩個部分：第一部分為使用花東、信義、竹崎、金門、名古屋與石岐六個保育品種，模擬系譜缺失時，從已知親本數目之世代，以迴歸插補法 (regression imputation)計算遺失值，再利用種親數目計算累積近親係數，探討保種族群近親係數累積之程度。結果顯示，模擬近親係數比實際值平均僅低估0.16%。因此進一步以同樣方式計算保育品種自基礎族群累積至今的近親係數。結果顯示保育品種近親係數已累積到一定程度。其中最高為信義，達56.7%，其次為竹崎 (52.0%)、金門 (37.0%)、石岐 (36.7%)、花東 (36.0%)，最低為名古屋 (26.3%)。第二部分使用保育品種從2002年至2012年之產蛋資料與系譜進行遺傳分析，並以選拔總產蛋數之L2品系作為對照，進一步探討利用避免全、半同胞配種的保育品種其產蛋性能是否因近親配種而產生近親衰退的現象。表現型結果顯示，金門比其他保育品種有較早的初產日齡及較多的總產蛋數，而產蛋週期、休產期性狀在保育品種間各有差異；L2在產蛋週期性狀表現皆較保育品種長，但休產期性狀無明顯較短。為進行遺傳分析，須將未呈常態分布的產蛋性狀以Box-Cox轉型成常態分布。利用個體育種價計算各族群各產蛋性狀在每世代之遺傳增加量，L2有隨世代數目而明顯改善，在保育品種方面，除了金門與名古屋沒有改變以外，其餘品種均有改善的趨勢。在近親係數每增加10%時，保育品種總產蛋數之育種價有顯著的增加，顯示保育品種目前仍不受到近親衰退的影響，且有因為自然選拔而間接改善產蛋性狀的現象。To maintain genetic diversity is a major topic in conservation. Plentiful genetic resources are an important key for the development and improvement of livestock. Therefore, maintaining genetic diversity is necessary while conserving a population. Inbreeding coefficient (F) is the main message to conserve a breed and it was estimated from pedigree information. For a long-term maintained population, data may be lost with a poor management or the mating scheme changed. Hence, it may make the F estimation biased or even cannot be estimated. Local chicken may extinct because of poor production performance as compared with highly efficient commercial breeds. It is essential to conserve these breeds, but conserve them in small population may cause inbreeding depression and loss of genetic diversity. This study includes two parts. In Part 1, data from six conserved breeds, Hua-Tung, Hsin-Yi, Ju-Chi, Quemoy, Nagoya and Shek-Ki were used. Regression imputation method was used to estimate numbers of parents in missing generation based on the information of other generations. The results showed that on average the simulated F value only underestimated 0.16% of the real value, so the same method was used to calculate the cumulative F value in six conserved breeds from the base population. The result found that F values of all six conserved breeds were substantial and the highest was shown in Hsin-Yi (56.7%) following by Ju-Chi (52.0%), Quemoy (37.0%), Shek-Ki (36.7%), Hua-Tung (36.0%) and the lowest was Nagoya (26.3%). In Part 2, pedigree and egg production data from 2002 to 2012 of six conserved breeds were used to estimate inbreeding coefficient (F) and breeding value (EBV) and results were compared with L2 strain which is selected for egg production. Results of phenotypic traits showed, Quemoy had the earlier age at the first egg and more total egg number than other conserved breeds. Clutch and pause lengths of egg production were different among conserved breeds. L2 had longer clutch length, but pause length was not shorter than conserved breeds. In order to do genetic analysis, data not normally distributed were normalized using the Box-Cox transformation. Linear estimates of genetic gain per generation of every trait were calculated from individual breeding values for every population. For the egg production traits, L2 strain had substantial improvement, and for the conserved breeds, except for Quemoy and Nagoya without any change, all the other four conserved breeds showed a trend of improvement. For the changes in EBV per 10% F, total egg number had trend of improvement on average among six conserved breeds. The results showed no inbreeding depression was found in these conserved breeds, and natural selection might have an indirect effect to improve their egg production traits.壹、前言 1 貳、文獻探討 3 一、 系譜配種 3 (一) 近親係數 3 (二) 系譜不完整之影響 5 (三) 插補法的介紹 6 (四) 估計近親係數的發展 7 二、 近親配種對產蛋性能的影響 10 (一) 雞隻產蛋性狀 10 (二) 近親配種與近親衰退 13 三、 變方成分及遺傳參數的估計 14 (一) 變方成分 15 (二) 遺傳參數估計 21 四、 雞隻種原保存現況 23 (一) 花東雞 (Hua-Tung chicken, HT) 24 (二) 信義雞 (Hsin-Yi chicken, HY) 24 (三) 竹崎雞 (Ju-Chi chicken, JC) 27 (四) 金門雞 (Quemoy chicken, KM) 27 (五) 名古屋雞 (Nagoya chicken, NG) 30 (六) 石岐雞 (Shek-Ki chicken, SK) 30 (七) L2品系 (L2 strain) 33 參、材料與方法 36 一、 資料來源 36 二、 系譜資料分析 36 (一) 系譜資料 36 (二) 近親係數 39 三、 產蛋資料分析 41 (一) 產蛋資料 41 (二) 統計分析 42 四、 遺傳趨勢 47 五、 近親衰退 48 肆、結果與討論 49 一、 系譜資料分析 49 (一) 使用不完整系譜資訊估計近親係數 49 (二) 以種親數目估計近親係數 51 二、 各族群產蛋性狀表現型比較 56 (一) 初產日齡 56 (二) 總產蛋數 56 (三) 產蛋率 56 (四) 產蛋週期性狀 56 (五) 休產期性狀 57 三、 Box-Cox轉型 64 (一) 原始資料常態性檢定 64 (二) Box-Cox轉型結果 66 四、 產蛋性狀之遺傳參數估計 70 五、 各族群產蛋性狀之遺傳趨勢 72 六、 近親配種對產蛋性狀之影響 78 伍、結論 81 陸、參考文獻 82 柒、附錄 9

Hydrothermal Growth of Quasi-Monocrystal ZnO Thin Films and Their Application in Ultraviolet Photodetectors

Quasi-monocrystal ZnO film grown using the hydrothermal growth method is used for the fabrication of Cu2O/ZnO heterojunction (HJ) ultraviolet photodetectors (UV-PDs). The HJ was formed via the sputtering deposition of p-type Cu2O onto hydrothermally grown ZnO film (HTG-ZnO-film). The effect of annealing temperature in the nitrogen ambient on the photoluminescence spectra of the synthesized ZnO film was studied. The optoelectronic properties of Cu2O/ZnO film with various Cu2O thicknesses (250–750 nm) under UV light (365 nm; intensity: 3 mW/cm2) were determined. The UV sensitivity of the HTG-ZnO-film-based UV-PDs and the sputtered ZnO-film-based UV-PDs were 55.6-fold (SHTG) and 8.8-fold (Ssputter), respectively. The significant gain in sensitivity (SHTG/Ssputter = 630%) of the proposed ZnO-film-based device compared to that for the device based on sputtered film can be attributed to the improved photoelectric properties of quasi-monocrystal ZnO film

Bulletin municipal officiel de la ville de Paris. Délibérations des assemblées de la Ville de Paris et du Département de la Seine. Conseil municipal de Paris

19 février 19541954/02/19 (N26,A74)

Additional file 8: Table S7. of Transcriptomic analyses of regenerating adult feathers in chicken

cEF vs. cMF differentially expressed gene set (shown in FPKM and fold change). (XLSX 86 kb

Additional file 5: Table S4. of Transcriptomic analyses of regenerating adult feathers in chicken

Positively selected and/or rapid evolving genes in avian lineages [29] that are expressed in all feather samples. (XLSX 11 kb

Additional file 12: Table S11. of Transcriptomic analyses of regenerating adult feathers in chicken

Canonical pathways for cEF vs. cMF differentially expressed gene set. (XLS 46 kb