A Novel Procedure to Identify Genes involved in Electron Transfer of Exoelectrogens
Purpose of research. Microbial fuel cells (MFCs) are bioelectrochemical systems that generate electrical energy by exploiting the extracellular electron transport (EET) capabilities of electrochemically active bacteria (EAB) (Logan 2009). This investigation aims to identify genes involved in driving bacterial EET with a new procedure that enables rapid screening of a side array of genes. These insights may lead to improved MFC performance through enhancing reactor design or genetic engineering EABs (Alfonta 2009). Procedures. MFC metagenomic analysis. Twelve MFCs incubated with four different bacterial samples were operated for approximately one year. The bacterial DNA from before and after incubation was extracted and the 16S rRNA regions were PCR amplified and sequenced. The bacterial community changes were analyzed using the QIIME program to identify bacteria that were being selected. Fosmid Clone Isolation. An E. coli fosmid library (Mewis et al. 2013) that contained genes from EAB inferred in the previous step was incubated in three MFCs. After a 48 hour enrichment period, biofilm samples from the MFCs were extracted and individual clones were isolated and screened in the MFCs individually. An E. coli DH5α strain with no insert DNA was incubated separately as the control. DNA sequencing. Fosmid insert DNA from high-performing clones were extracted, purified using gel electrophoresis, constructed into sequencing libraries and sequenced. Bioinformatics Analysis. The sequences were constructed into larger contigs using the Velvet algorithm package. The open reading frames (ORFs) were inferred and translated into amino acid sequences and annotated with proteins identified from the KEGG, and SEEDs databases using Metapathways 2.5. Results. The changes in bacterial communities from the metagenomic analysis revealed increases in relative abundance in numerous genera from Firmicutes and Bacteroidetes. The MFCs incubated with the fosmid clones generated about 4 times more peak power than the MFCs incubated with the E. coli DH5α. Polarization curves generated for the MFCs demonstrated that the fosmid clones were able to sustain a higher current. Incubation of pure cultures of individual clones yielded four clones with significant performance improvements over the control strain. Protein data from Metapathways outputs reveled both novel and previously reported EET genes encoding for Type IV pilus structures, c-type cytochromes, soluble cytochromes, flavoproteins, and porins. Taxonomy inferences of the gene inserts by the Green Genes database reveal the genes most likely came from the same EABs that were inferred from the metagenomic analysis. Conclusions. The increased performance of the fosmid clone-powered MFCs suggest that the clones carried genes that enhanced their performance in the MFCs. This is further confirmed by polarization curves generated for the MFCs. The results of the taxonomy inferences suggest that the bacteria being selected for in the environmental samples carried genes that enhanced their performance in the MFCs, and that these genes were successfully identified in the subsequent steps. The results of this study demonstrate that using a gain of function approach to rapidly screen a wide array of genes in a gene library may be an efficient method to identify genes that enhance power generation of EABs in MFCs.
蛙！到底發生了什麼事？探討溪谷生態系畸形蛙的發生原因及其生態學之研?
Our research started from June, 2003 to May, 2004. During these twelve months, we collected and discussed the basic ecology material of malformed “ Rana latouchii ”, which we call it frog in the following paragraphs . Thanks for the favorable geographical position, we collected the first-hand data in the area of Jin-Mian Mountain foothill gully situated in Taipei. Our investtigation project includes：the percentage of the malformed frogs in a whole race, the geographical distribution of dominant-abnormal frogs, the sexual distribution of dominant-abnormal forgs, and the possible roots for the generation of malformed frogs. We have altogether carried seventy-six times field investigations. In those investigations, we focused our research on the randomly-sampled 580 Rana latouchii. In these 580 sample, there are 190 female, 350 male, and 40 adolescent. We discovered seventy-six malformed frogs, constituteed by 21 female, 53 male and 2 adolescent. In another words, the occurance of malformed frog in a race is around 13.1. %. In our observation, we can classify dominant-abnormal frogs, “Rana latouchii”, into eight species. Here are the species: 1. the entire body is obviously malformed, 2. with only one eye, 3. in lack of appendage apod, 4. in lack of arms,5. in lack of palms, 6. with excess webbed toes, 7. the maltfromed of appendiculars, 8. the lack of toes on the palms. Within these 8 species, the last species has the highest occurance, 66.38% in aproximation. If we look at the classfication by sex, the ratio of female to male is around 1 to 2.52(1:2.52). However, the possibility of being maleformed is regarded as the same for female and male frogs in the same group. In statistical term, our research shows that the chi-square is 1.742 while our degree of freedom is 1 and confidence level is 95% (X2=1.742，df=1，p>0.05). During the research, we also observe that each malformed species affect different living activities of malformed frogs. In the worst situation, the malformed nature can result in shorter life. In our sampling area, malformed frogs mostly reside in high concealment and high humidity location. In our research data, within these area, our re-captured rate for malformed frogs is 25% and hirudin-parastical rate is 4.31%. As our research shows, the occurance of malformed “Rana latouchii” in our selected area results from 3 main causes： First, the parasitism of leeches or parasitic worm；Second, the agriculturally chemical contaminants；Third , the injured causes from escape from predator. 本研究自2003年6 月至2004年5月為止，共12個月的期間，於臺北市內湖區金面山南麓溪谷，對拉都希氏蛙(Rana latouchii)族群之畸形蛙個體進行基本生態資料的蒐集與探討，調查項目包括：族群中畸形蛙發生的比例、畸形蛙外部形質異常分佈的情形、族群中雌蛙與雄蛙發生外部形質異常之情況及可能造成畸形蛙產生的原因。 研究期間共進行了76次的野外調查，總紀錄了拉都希氏蛙580隻，雌蛙有190隻，雄蛙有350隻，幼蛙有40隻；畸形蛙個體共紀錄有76隻，雌性畸形蛙有21隻，雄性畸形蛙有53隻，幼體畸形蛙有2隻。族群中畸形蛙發生率約為：13.10％，外部形質異常的畸形拉都希氏蛙總計有八大類，包括：1.整隻個體形質畸形，2.單眼個體，3.附肢缺少，4.附肢缺臂，5.附肢缺掌，6.腳掌多趾，7.附肢腳掌畸形，8.附肢腳掌缺趾，其中以附肢腳掌缺趾類的66.38％發生率最高。畸形蛙中雌雄比約為1：2.52，族群中雌蛙與雄蛙發生畸形的比例並無顯著的差異（X2=1.742，df=1，p>0.05）。 不同部位形質畸形的發生，將會影響畸形蛙的個體活動，甚至可能降低畸形蛙的存活機率。研究調查樣區中，畸形蛙較常活動於濕度高且隱蔽度大的分樣區中，畸形蛙的重複捕捉率為25％，被水蛭寄生的比例則約是4.31％。 由調查研究結果顯示，造成內湖金面山區南麓溪谷拉都希氏蛙畸形蛙發生的主要原因，推測可能有下列幾種：(1)水蛭或是吸蟲類的寄生；(2)農作過程中的化學污染物；(3)逃脫掠食者捕食過程受傷。
「金」枝「玉」葉—金奈米與葉綠素的交互作用
本實驗在探討，當金奈米粒子和植物中的葉綠素產生鍵結作用力時，能量轉移的結果是否能幫助葉綠素激發電子。經由兩者混合後光譜的變化,發現兩者之間發生能量轉移。為探討此轉移現象和濃度的關係，我們將大小不同的金奈米和不同毫升數的葉綠素作用，並將其結果和金奈米與葉綠素的吸收強度和作比較，使用正規化的計算方法算出比值，由此看出兩者之間能量轉移的效率。當金顆粒約大於30nm時，正規化的數值隨的葉綠素濃度的增加而變大；而當金奈米顆粒約小於30nm時，則隨著葉綠素的增加而變小。Much attention is currently focused on chromophoric molecules because they can not only mimic natural antenna systems but also exhibit unique optical and physical properties. Chlorophyll , produced by extracting from green leaves, has electrostatic interactions with Au nanoparticles through carboxyl groups. Herein, we report the charge transfer between chlorophyll and Au nanoparticles using UV-vis electronic absorption spectroscopy. The efficiency of charge transfer from chlorophyll to Au nanoparticles was estimated by the normalization of Q-ban absorption intensity. From the observation of absorption intensity versus concentration of chlorophyll curves, we find that the efficiency of charge transfer is increased while the size of Au-particle is larger than 30nm, but decreased while the size smaller than 30nm.
氣泡在黏滯性液體中的運動
本研究目的在探索不同大小之氣泡在不同黏滯性液體中運動情形。實驗結果發現大氣泡向上運動的速度較大，其下方會漸漸向內凹。並且觀察到氣泡間結合時的相互作用：氣泡在相同黏滯性膠水中上升時，若下方氣泡體積較大，其較快的速率會使距離縮短。此時小氣泡的下半向內凹，大氣泡的下半則向外呈現流線型尖端並且在接近小氣泡時速率增加，最後與小氣泡結合。若上方氣泡體積很小，與下方大氣泡的距離縮短至相互貼合，小氣泡會先停留在大氣泡的上半表面，再沿大氣泡表面下滑至大氣泡的下半才與大氣泡結合。This research traces the motions of bubble with different volume in viscid liquid. The experimental results show that the bigger bubble rises at faster speed. The shape of the small bubble is round. As the volume of the bubble increases, it turns hamburger-like. And if the bubble is big enough, its underside would be concaved. In viscid liquid, the speed of the bubble is not smooth but waved. The smaller the bubble is, the more the variation in speed is. The interaction of two bubbles is also studied. There are two types of the combination of two bubbles. While the big one closes to the small one, it is accelerated. The underside of the small one becomes concave. And the big one becomes streamline shape. If the difference in volume between two bubbles is significant, the small one slides along the surface of the big one, and goes into the concave beneath it, then combines with it.
Computer Vision for Alternative Input Systems
In the fast-paced environment of a hospital intensive care unit (ICU), good doctor-patient communication is essential. However, medical conditions and devices often inhibit a patient’s ability to speak, write or type. Current assistive communication devices are either prohibitively expensive or cumbersome and time-consuming, creating a gap in communication during a patient’s first days in the ICU. This project applies computer vision to develop a low-cost software solution that bridges this gap by enabling patients to generate words with eye movements. In the system, a webcam acquires an image of the patient, and an image processing algorithm classifies patient’s gaze as pointing in one of eight directions. Each direction corresponds to an option on a graphical menu presented to the patient on the computer’s display. The patient can use the menu to select a preformed phrase from a list of common phrases. Patients desiring to express more complex ideas can type custom words using the menu as an ambiguous keyboard (similar to a phone keypad). In either case, the patient-generated text will be displayed on screen and read aloud through the computer’s audio system. The only hardware requirements are an existing computer and a $6 webcam. The program can process and respond to an image in 148ms. A new user can be trained in approximately 10 minutes, and after training can type a simple phrase such as “hello world” in 40 seconds. While further testing and improvement is required before the system will be ready for implementation, the project shows promise as a low-cost solution to ICU communication.
大安水蓑衣(Hygrophila pogonocalyx)的復育對黑擬蛺蝶(Junonia iphita iphita)食性偏好??
大安水蓑衣（Hygrophila pogonocalyx）為局限分佈於臺中縣沿海溼地之稀有植物。大量境外復育栽殖後，造成近年來黑擬蛺蝶(Junonia iphita iphita)利用此種新寄主植物的比例增加。本實驗比較黑擬蛺蝶在原寄主植物臺灣馬藍(Strobilanthes formosanus)及新寄主植物大安水蓑衣上之生長環境遮蔽度、幼蟲生長發育、雌蝶產卵偏好的差異，探討大安水蓑衣復育對黑擬蛺蝶族群可能造成的影響。實驗結果發現利用大安水蓑衣之幼蟲生長發育較佳、羽化後成蟲體型較大、有效積溫常數較低。雌蝶產卵行為可能存在兩種偏好性，且子代雌蝶對寄主植物的偏好性與親代一致，不受幼蟲期取食植物影響。偏好新寄主植物之雌蝶其子代的生長發育，利用新寄主植物者顯著較利用原寄主植物者佳，顯示其對原寄主植物的適應顯著下降。本研究認為大安水蓑衣的復育結果，造成黑擬蛺蝶族群在可能共域的情況下，因為利用新的寄主植物可能已產生初步分化的現象。Hypgrophila pogonocalyx is a rare plant species which is distributed in wetlands along seashore of Taichung County. Recently, I found that the common butterfly Junonia iphita iphita recognized H. pogonocalyx as a new hostplant because of the restoration practices of H. pogonocalyx. We compared the differences of forest overstory coverage, larval growth performance and female oviposition preference between J. iphita iphita individuals exploiting the H. pogonocalyx and those utilizing the original hostplant Strobilanthes formosanus. Possible effects on J. iphita iphita by restoration of H. pogonocalyx are analyzed and discussed. It turns out that better growing performance and longer adult forewing length were found on the larvae feeding on H. pogonocalyx than those on the S. formosanus. Besides, the larvae feeding on H. pogonocalyx demonstrated lower constant value of effective accumulated temperature, suggesting that the new host may provide more energy to the larvae than the original host does. Two types of female oviposition preference seem to exist. No matter which hostplant the larvae fed on, the female adults still maintained the oviposition preference of the parental generation. Offspring of H. pogonocalyx-preferring female had better performance on this new hostplant. Our studies showed that the restoration of H. pogonocalyx might have caused primary differentiation of J. iphita iphita by using new hostplant in sympatry with the original hostplant.
DNA Detection by EGFET using GaN Nanowires Gate
DNA感測器近年來蓬勃發展,應用層面包括基因工程,醫學及藥物的開發等,然而目前較常使用的感測方法,需要繁瑣耗時的標定過程,且所使用的化學藥劑對環境容易造成傷害,鑒於以上方法的不完善處,我們決定設計一套新的感測系統,此研究結合了氮化鎵奈米線(GaN Nanowires)及延伸場效電晶體(EGFET)的優點,成功的發展出創新的DNA感測系統,氮化鎵奈米線的高生物匹配性及高感測面積,能有效提高靈敏度,延伸式場效電晶體的設計,史感測器具由免標定及時感測的特性,且易於組裝及操作,我們將探針DNA(probe DNA)修是在氮化鎵奈米線作為之延伸閘極上,由於DNA在中性水溶液中帶負電,且DNA之間具有強烈的互補特性,因此當目標DNA(target DNA)與探針DNA接合,形成雙股DNA,氮化鎵奈米線(閘極)的表面電位即會有所變化,並造成FET特性的改變,藉由此性質及能成功感測DNA,研究結果顯示,此研究所發展出的DNA感測器,愈有相當高的靈敏度(10-18),相較於其他以FET技術所設計出的DNA感測器,靈敏度提升了三個數量極,此外此感測器亦具有高選擇性,即使單一鹼基對的突變也能成功辨別;-hybridization based detection techniques are widely developed due to their promising applications in genetics, medicine and drug discovery. However, current DNA detection techniques based on labels or reagents are time-consuming, environmentally-harmful and complex to implement. In this study, we have successfully demonstrated a label-free extended-gate-field-effect-transistor (EGFET) sensor utilizing a GaN-nanowires electrode with DNA probes immobilized, capable of specific DNA sequence identification. The principle behind the design is based on the change in surface potential and charge transfer after hybridization. GaN nanowires, being bio-compatible, provide direct transfer path and high surface area, thus offer an unprecedented opportunity of DNA sensing with high sensitivity. In addition, our EGFET design facilitates easy assembly and operation of DNA detection. Comparative studies on complementary and non-complementary DNA were performed to verify the specificity of the sensor. By adapting GaN nanowires structure, the assay time of DNA was shorten to within thirty minutes. Moreover, our sensor displayed an ultra-high sensitivity in the level of attoM: three orders of magnitude higher in resolution than that of other FET-based DNA detection methods.
生生不息-正五邊形的繁衍及算術法則
This study was to explore the nature of two basic constitutes of the regular pentagon,With these two constitutes, the regular pentagon could be multiplied into any times in size. We used four multiplication methodsto show how the regular pentagon enlarge and to verify that the enlarged regular pentagons derived from computer did exist. By integrating these four multiplication rules, we were able to arrange regular pentagon of any length of side, and evidenced the equation was ( If m,n is the number of A,B of a regular pentagon respectively ) When we tried to verify if any regular pentagon could be constituted by other smaller regular pentagons, we found that it was un-dividable only if the length of pentagon side were (the number of A, B were the 2n and 2n-1 item of Lucas Sequence), otherwise, any regular pentagon is able to be constituted by other smaller regular pentagons. The divided forms could be multiple. We also found that any pentagon could be divided by two successive un-dividable pentagons, which is called “standard division rule”. We expected to derive all kinds of division by analysis of two successive un-dividable pentagons in standard division rule.
這個研究起源於一個拼圖玩具：利用兩種黃金三角形排出指定大小的正五邊形。我們的研究動機是：一、 假如無限量供應A 和B，能夠拼出哪些邊長的正五邊形？二、 哪些拼好的正五邊形不能拆成一些較小的正五邊形？我們將研究的主要結果分述如下：