...正如你可能观察到的：
这是我的 LaTeX 代码：
\documentclass{bioinfo}
\pubyear{2014}
\copyrightyear{2014}
\usepackage{hyperref}
\usepackage{natbib}
\newcolumntype{L}{>{\centering\arraybackslash}m{3cm}}
\usepackage{booktabs, multicol, multirow}
%\usepackage{float}
%\usepackage{round}
\copyrightyear{2014}
\author{Jeffrey Wubbenhorst}
\usepackage{graphicx}
\begin{document}
\firstpage{1}
\title[ ]{Analysis of Prothrombin G20210A in Relation to VTE}%{Visualization}
\author{Jeffrey Wubbenhorst}
\address{ 1219 Broad St, Durham, NC 27705}
\history{Received on May 28th}
\editor{Mr. Robert Gotwals}
%\section{Contact:}\href{Jeffrey Wubbenhorst}{[email protected]}
\maketitle
\iffalse
\documentclass{bioinfo}
\copyrightyear{2014}
\pubyear{2014}
\usepackage{graphicx}
\begin{document}
\firstpage{1}
\title[QTL Analysis]{Evaluation of a QTL Dataset}
\author[Robert R. Gotwals]{Robert R. Gotwals\,\footnote{to whom correspondence should be addressed}}
\address{$^{1}$Department of XXXXXXX, Address XXXX etc.}
\history{Received on XXXXX; revised on XXXXX; accepted on XXXXX}
\editor{Gotwals}
\maketitle
\fi
\begin{abstract}
Computational biology methods were used to visualize the structure and function of prothrombin and thrombin and their interaction with their enzymes and substrates. In addition, exploratory analyses of the theoretical physiologic effects of the prothrombin G20210A mutation in the gene were carried out. These interactions were modeled using the computational methods. This mutation results in abnormally high levels of prothrombin, which in turn lead to higher risks for thrombotic events such as deep vein thrombosis, heart attack, stroke, and pulmonary embolism. Finally, BLAST was used to create a phylogenetic tree of the F2 gene and its variants. clinical outcomes can be improved using thrombin inhibitors and anticoagulants.
\section{Keywords:} \textit{thrombin, G20210A, prothrombin, BLAST, Molegro, }
\iffalse
\section{Results:}
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation
\fi
%\section{Contact:} \href{[email protected]}{[email protected]}
\end{abstract}
\section{Introduction}
%State clinical relevance!
%Venous thromboembolisms are is a
\subsection*{Coagulation Cascade}
%This needs to be described in greater detail.
The coagulation system is one of the most important physiologic systems in humans. %Explain importance of coagulation cascade.
The coagulation system balances thrombosis (clotting) thrombolysis (inhibition of clotting) and regulation of platelet function. in order to provide homeostasis and cellular injury, tissue damage and bleeding. %Explain the role of platelets here
The coagulation cascade is one of the most important physiologic systems. It balances thrombosis (clotting), thrombolysis (inhibition of clotting), and regulation of platelet clotting in order to provide homeostasis and protection against cellular damage, tissue damage and bleeding.
The coagulation cascade is a series of processes which lead to the formation of fibrin. (Figure \ref{pathway}) Figure \ref{pathway} is a simplified pathway illustrating the coagulation cascade (image courtesy of Santa Barbara City College).
Fibrin is a protein formed by the interaction between thrombin and fibrinogen. Thrombin, a serine protease, is part of a class of enzymes that cleave peptide bonds in proteins, and is formed from prothrombin by the action of the enzyme prothrombinase (also known as Factor X or thrombokinase). %Add in where proteins are produced, what regulates their production, discuss platelets, where they come from
Prothrombin is a precursor of thrombin, and is encoded by the F2 gene (HGNC ID 3535), located on 11p11.2. Thrombin interacts with at least a dozen substrates, and plays a crucial role in the coagulation cascade. It exists in two forms, inactive and activated.
An accumulation of fibrin results in the formation of blood clots (thrombosis); since fibrinogen is activated by thrombin to produce fibrin, excessive amounts of thrombin (and by extension prothrombin) increase risk for VTE. \cite{unknown} %I think the cartoon rendering is best, and industry standard
Figure \ref{thrombin} is a rendering of the secondary structure of thrombin, as rendered from PDB ID 2HGT. Figure \ref{prothrombin} is a cartoon rendering of the secondary structure of prothrombin from PDB ID 1PPB.
%\iffalse
\subsection*{Venous Thromboembolism}
A venous thromboembolism (VTE) occurs when a blood clot (or thrombus) forms inside a vein. If thrombus forms within a vein deep in the body, it is called a deep vein thrombosis, or DVT. These are dangerous because they can: (1) increase in size, blocking circulation (2) travel to the lungs, causing a pulmonary embolism, and (3) travel to the brain causing stroke. A wide variety of risk factors are involved in venous thromboembolism, including genetic factors, long-distance travel, and lifestyle. \cite{Hematology} For the purposes of this evaluation, we will be focusing on the influences of G20210A on VTE, which has been associated with major morbidity. Fatal recurrences occur in between 5\% 9\% of patients, causing a significant economic burden to the health care system. \cite{burden, protocol,factors} Clinical trials indicate that heparins can be used to treat some expressions of VTE, though it is not clear if these had any significant influence on mortality. \cite{treatment,PE}
%\fi
\iffalse
\begin{center}
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.25]{fibrinogen.png}
\caption{\textit{Fibrinogen (rendered from PDB 1M1J)}}
\label{fibrinogen}
\end{figure}
\fi
%I got the image here: http://www.biosbcc.net/doohan/sample/htm/Hemostasis.htm
\subsection*{The Prothrombin G20210A Mutation}
%Discuss blood clots!
%should I talk about how proteins are manufactured?
The prothrombin G20210A mutation in the F2 gene on chromosome 11 is a genetic variant that increases risk for thrombosis. The F2 gene was originally discovered by Poort, Rosendaal, Reitsma, and Bertina in 1996, and has been well-characterized. \cite{pmid8916933} Along with factor VII, IX, and X, prothrombin is theorized to regulated by molecular mechanisms. \cite{stability} The gene codes for prothrombin (also referred to as coagulation factor II). Prothrombin G20210A (also known as the factor II mutation, or the prothrombin mutation) is a genetic variant of F2, and is the result of a single nucleotide polymorphism, a guanine-adenine switch at F2 position 20210. \cite{sequence} The polymorphism occurs on the noncoding region of the prothrombin gene at position 20210. \cite{pmid8916933} Figure \ref{f2} shows the location of the gene on chromosome 11 (image courtesy of the National Institutes of Health). The G20210A mutation leads to elevated levels of prothrombin, which contributes to hypercoagulability; the latter increases the risk of VTE. Thrombin is also a part of the negative feedback cycle for the coagulation cascade, and abnormal levels thrombin and prothrombin inhibit the normal regulation of blood clotting in multiple ways.
The G20210A mutation occurs primarily in males, and almost exclusively in Caucasians, with roughly 3\% of the population carrying the gene. \cite{JTH3394, Rosendaal01012005} The mutation has also been associated with obstetric complications and miscarriages. \cite{Obstetric, miscarriage}
%I need to explain what active and inactive forms are! I also need to state how it gets from the inactive to the active states
%Do I need to mention prothrombin time?
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.5,angle=270]{F2.jpg}
\caption{\textit{Cytogenic Location of F2 Gene on Chromosome 11}}
\label{f2}
\end{figure}
%Prothrombin time is a derived measure qunatifying the coagulation time of blood.
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.25]{half_thrombin.png}
\caption{\textit{Thrombin in the Process of Activation}}
\label{half}
\end{figure}
\iffalse
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.15]{Thrombin_Shot.jpg}
\caption{\textit{Active and Inactive Forms of Thrombin}} %What makes these active and inactive?
\label{Active}
%This is a visualization in Molegro of 1MKX.
\end{figure}
\fi
\subsection*{Molecular Function of G20210A}
The molecular function of the G20210A mutation is not well understood. Kuwahara et al state that
\begin{quotation}
\textit{``Although prothrombin G20210A variant was first found in 1996 as a genetic risk factor of thrombosis, the underlying molecular mechanism for elevation of circulatory prothrombin levels due to the variant has remained elusive."} \cite{MitsuhiroKuwahara11162004}
\end{quotation}
The mechanism by which the G20210A mutation increases thrombotic risk is not well understood. There are three main hypotheses regarding the molecular function of the G20210A mutation:
%Are there really three?
\begin{enumerate}
\item \textit{\textmd{The G20210A mutation leads to higher levels of mRNA expression, leading to higher protein production}}
\item \textit{The G20210A mutation leads to efficiency gains in F2 3' end cleavage signal} \cite{recognition}
\item \textit{The G20210A mutation increase mRNA instability}
\end{enumerate}
While a consensus has not yet been reached in regards to the method by which G20210A leads to higher prothrombin expression, there is a data supporting the hypothesis that the mutation does not lead to mRNA instability as previously thought.
%I think this may need some more data...
\begin{methods}
\section{Methods}
% I think I need to reconcile my methods with my computational approach...
%Why is the text formatted differently in the methods section?
\subsection*{Computational Approach}
This investigated used computational biology methods (as noted above) to visualize thrombin structure and function and to model its activity in the coagulation system.
%Finish this later! It is worth noting that this 35% of this grade...
BLAST, the Molegro virtual docker, and the RCSB Protein Data Bank were all utilized to obtain a greater understanding of the coagulation cascade. A comprehensive overview of the F2 gene and the coagulation cascade was accomplished using the RCSB Protein Data Bank, and the NCBI Sequence Viewer.
\subsection*{Thrombin Pathway}
Pathways for thrombin and warfarin were used to visualize normal coagulation cascade pathways. %Make sure this section is typo-free!
\textit{\textbf{INCLUDE PATHWAYS WITH CAPTIONS}}
\subsection*{BLAST}
% BLAST (Basic Local Alignment Search Tool) was used to identify genetic sequences similar to the healthy F2 sequence. A table with similar sequences is shown below: %This needs to be phrased better.
Analogues to the the F2 gene (NCBI reference sequence NC\_000011.10) were compared using the NCBI BLASTN 2.2.29 algorithm. \cite{algorithm} Compared sequences were then used to create a phylogenetic tree to examine the development of the human prothrombin gene. BLAST data are shown in figure \ref{BLAST}. The phylogenetic tree is shown in figure \ref{Tree}.
\iffalse
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.4, angle=90]{Tree.png}
\caption{\textit{Phylogenetic Tree of BLAST Results}}
\label{Tree}
\end{figure}
\fi
\end{methods}
\section{Results and Discussion}
The G20210A mutation has a significant and unique influence on the proper function of the coagulation cascade, though the mechanism by which it does so is not presently understood.
\subsection*{BLAST}
Results from BLAST are shown in figure \ref{BLAST}.
\vspace{1cm} %I'm adding some space in to keep things from looking cramped.
\begin{figure}[ht!]
\begin{tabular}{|p{3cm}|p{0.75cm}|p{1.25cm}|p{1.75cm}|p{0.75cm}|}%{r|r|r|rr}
\toprule
\textit{\textbf{Description}} & \textit{\textbf{Max Score}} & \textit{\textbf{Total Score}} & \textit{\textbf{Accession}} & \textit{\textbf{Query Cover}} \\
\midrule
Coagulation factor II (thrombin) (F2), RefSeqGene on chromosome 11 & 37515 & 71435 & NG\_008953.1 & 100\% \\
\hline
Chromosome 11, clone RP11-792G9 & 37525 & 1.85E+05 & AC115088.6 & 100\% \\
\hline
Coagulation factor II (thrombin) (F2) gene, complete cds & 37382 & 65528 & AF478696.1 & 100\% \\
\hline
F2 gene, complete cds, Alu and KpnI repeats & 36596 & 68303 & M17262.1 & 100\% \\
\hline
Human gene encoding 5 exons of prothrombin. Exon 1 starts with amino acid position 144 and exon 5 & 8991 & 11357 & V00596.1 & 35\% \\ \hline
Homo sapiens genomic DNA, chromosome 11 clone:RP11-783K16, complete sequence & 761 & 1.28E+05 & AP001453.6 & 31\% \\
\hline
Human DNA sequence from clone RP5-1121G12 on chromosome 20, complete sequence & 756 & 80131 & AL109965.34 & 33\% \\ \hline
Homo sapiens BAC clone RP13-612N21 from 4, complete sequence & 752 & 18352 & AC092458.5 & 22\% \\ \hline
Homo sapiens chromosome 19 clone CTC-483I11, complete sequence & 743 & 1.68E+05 & AC008532.7 & 31\% \\ \hline
Homo sapiens genomic DNA, chromosome 11 clone:RP11-21A7\_A, complete sequence & 743 & 63866 & AP006333.1 & 32\% \\
\bottomrule
\end{tabular}%
\caption{\textit{BLAST Results}}
\label{BLAST}
\end{figure}
\vspace{1cm} %I'm adding some space in to keep things from looking cramped.
BLAST results suggest that there are few documented mutations of the F2 gene. The returned sequences are almost all different versions of the F2 gene, with the exception of AL109965.34 (a PHD finger protein), chromosome 19 clone CTC-483I11, and clone RP5-1121G12.
\subsection*{Phylogenetic Tree}
Figure \ref{Tree} is a phylogenetic tree as computed using BLAST pairwise alignments. The graphic indicates the similarities between the analyzed genes.
Prothrombin is cleaved by prothrombinase at arg$^{320}$ and arg$^{271}$, which leads to the A-chain and B-chain. The A-chain is non-proteolytic (does not cleave proteins), while the B-chain contains the active sites His57 (histidine-57), Asp102 (aspartic acid 102), and Ser195 (serine 195). The B-chain is known as thrombin. \cite{A_chain} One of thrombin's most important functions is the cleavage of fibrinogen at the N-termini of its A and B chains. This produces a fibrin monomer that can cross-link to itself, producing clot. \cite{pmid10528826, parts,JTH:JTH1363}
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.4, angle=90]{Tree.png}
\caption{\textit{Phylogenetic Tree of BLAST Results}}
\label{Tree}
\end{figure}
\subsection*{Visualization}
The effects of abnormally high levels of thrombin were examined graphically using the Molegro virtual docker. %, which was used to identify points at which ligands
As noted above, the F2 gene codes for prothrombin, which is cleaved at two different sites by activated Factor X (also referred to as Xa or prothrombinase) at arg$^{320}$ and arg$^{271}$. This leads to formation of the A-chain and B-chain. The A-chain is non-proteolytic (does not cleave proteins), while the B-chain contains the active sites His57 (histidine-57), Asp102 (aspartic acid 102), and Ser195 (serine 195). \cite{A_chain}
%Below is a rendering of the cleavage points of prothrombin:
Figure \ref{1FPH} is a rendering of the interaction between thrombin and fibrinogen. Alpha-chain thrombin is interacting with an analogue of fibrinopeptide A (a substance released when cleaved by fibrinogen) and a C-terminal hirudin peptide (an important factor in the electrostatic interaction with thrombin). \cite{cterminal} It should be noted that the molecules bind to each other in multiple places, which partially accounts for the extreme specificity of thrombin. \cite{specificity} The rendering in figure \ref{half} only involves a segment of fibrinogen.
\subsection*{Molegro Renderings}
Figure \ref{fibrinogen} is an illustration of the secondary structure of fibrinogen (as rendered from PDB ID 1M1J).
Figure \ref{Active} shows inactive thrombin (prothrombin) on the left, and activated thrombin on the right. Figure \ref{half} shows a rendered cartoon of thrombin in the activation process. Figure \ref{1FPH} illustrates the secondary structure of the interaction between thrombin and fibrinogen.
\begin{center}
\begin{figure}[ht!]
\includegraphics[scale=0.15]{1FPH_(Thrombin+fibrinogen).png}
\caption{\textit{Interaction Between Thrombin Fibrinopeptide A (rendering from PDB 1FPH)}}
\label{1FPH}
\end{figure}
\end{center}
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.25]{fibrinogen.png}
\caption{\textit{Fibrinogen (rendered from PDB 1M1J)}}
\label{fibrinogen}
\end{figure}
The active and inactive forms of thrombin (from left to right) are shown in figure \ref{Active}.
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.15]{Thrombin_Shot.jpg}
\caption{\textit{Active and Inactive Forms of Thrombin}} %What makes these active and inactive?
\label{Active}
%This is a visualization in Molegro of 1MKX.
\end{figure}
\begin{figure}
\centering
\includegraphics[scale=0.25]{Prothrombin.png}
\caption{\textit{Prothrombin (rendered from PDB ID 1PPB)}}
\label{prothrombin}
\end{figure}
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.25]{Thrombin.png}
%
\caption{\textit{Thrombin (rendered from PDB ID 2HGT)}}
\label{thrombin}
\end{figure}
\begin{figure}
\centering
\includegraphics[scale=0.4]{clottingcascade.jpg}
\caption{\textit{Overview of Coagulation Cascade}}
%This image is too shoddy.
\label{pathway}
\end{figure}
\subsection*{Molecular Function of G20210A Mutation}
The exact mechanism of the G20210A mutation is not yet well understood. Ceelie et al state that
\begin{quotation}
\textit{``...it seems less likely that mRNA stability plays a major role in explaining the differences between the levels of the two mRNAs, as there is no difference between the poly(A) tail between 20210A and 20210G mRNA... In conclusion, our data support the idea that the 20210A variation at the 3'-end of the prothrombin gene leads to enhanced 3'-end formation and increased mRNA and protein expression."} \cite[p.~361]{unknown}
\end{quotation}
The poly(A) tail is a chain of adenine nucleotides attached to the end of mRNA that increases mRNA stability. Over time, the tail slowly disintegrates, which leads to the enzymatic breakdown of mRNA. \cite{poly} The fact that the G20210A mutation has no effect on the length of the poly(A) tail is suggestive of another mechanism. A similar view is expressed by Pollack et al, who state that
\begin{quotation}
\textit{``Prothrombin mRNAs that are polyadenylated at position 20210 translate with higher efficiency than mRNAs polyadenylated at position 20212; consequently, 20210A mRNAs (which are all polyadenylated at the translationally active 20210 site) generate more prothrombin than an equal quantity of 20210G mRNAs (most of which are polyadenylated at the translationally quiescent 20212."} \cite{stability}
\end{quotation}
Pollak ete al extend this view slightly:
\begin{quotation}
\textit{``[Evolutionarily related coagulation factor including factors VII,
IX, and X, and protein C.25] factors are encoded by genes
derived from a common prothrombinlike progenitor gene and
possess related functional domains, raising the intriguing possibility
that their expression might be regulated through conserved
molecular mechanisms. "} \cite[p.~126]{stability}
\end{quotation}
\subsection*{Pathways}
Figure \ref{warfarin} shows a pathway for warfarin, a drug commonly used to mitigate symptoms of G20210A (image courtesy of PharmGKB).
\begin{figure}[ht!]
\centering
\includegraphics[scale=0.4, angle=90]{warfarin.png}
\caption{\textit{Warfarin Pathway}}
\label{warfarin}
\end{figure}
%What is a conserved molecular mechanism?
\section{Conclusions}
Bioinformatics played in integral part in the analysis of the G20210A mutation. Bioinformatics allows us the unique opportunity to observe clinical outcomes as the result of a single polymorphism. This study would not have existed without bioinformatics tools such as BLAST, and Molegro. %This statement will need to be examined again to see if it is appropriate.
\subsection*{Clinical Treatment for Effects of G20210A}
%Here, I will discuss possible treatments for G20210A.
The clinical effects of abnormally high levels of prothrombin due to G20210A can be mitigated in various ways. Anticoagulants (such as coumarin or warfarin) or direct thrombin inhibitors (such as Argatroban or hirudin) have been shown to increase positive outcomes. Emerging developments are being made in the field of new oral anticoagulants, though there is as of yet little information as to their improvement of clinical symptoms. \cite{anti} For VTE in particular, oral anticoagulants are
\section*{Acknowledgments}
Appreciation is extended to Mr. Robert Gotwals for his assistance in this project. This project was funded in part by the NCSSM Foundation. %Is this really something I would like to add in?
\bibliographystyle{unsrtnat} %Find a good way to neaten this up, maybe number my references.
\bibliography{document}
\end{document}
Thrombin is a serine protease, WHICH IS WHAT?
Pulmonary embolism has at times been associated with travel (see citation)
The G20210A mutation leads to higher levels of prothrombin, which leads,
I could take a prevention perspective
Illustrated demonstration of mutated thrombin's effects on cascade
I could look at how mutated thrombin increases the risk
from Bob Gotwals to Everyone:
jeffrey do you have a question?
from Jeffrey Wubbenhorst to Everyone:
My study is going well so far, but I'm not entirely certain of the depth to which I should go for this study.
from Jeffrey Wubbenhorst to Everyone:
I'm using Molegro, BLAST, and a few other things here.
from Bob Gotwals to Everyone:
it's a three week project, not a graduate school dissertatin
from Jeffrey Wubbenhorst to Everyone:
Condensed: Do I need to go into any greater detail than I did for a protein profile?
from Bob Gotwals to Everyone:
ok....you have to have some problem or system that you are studying, and ultimately describe how computing helped you understand whatever it is you are doing.
from Jeffrey Wubbenhorst to Everyone:
(Aside from longer iuntroductions and such)
from Jeffrey Wubbenhorst to Everyone:
OK, that really helps. The required length for this paper was 5-6 pages, right?
from Bob Gotwals to Everyone:
well, I won't know until I see it. It's about a 6 page paper, but I hate giving page limits because you all go absolutely crazy about page counts. you should create a reasonable document that demonstrates that you know something about the system you are studying, that you used one or more computing tools to study it, and you have some understanding of what your calculations did.
Alpha-thrombin is
1DWB is a crystollographically-obtained analysis of the binding to human thrombin of four active site-directed inhibitors.
F2r=thrombin
polymorphism leads to instability in mRNA
resulting in higher prothrombin
I am examining the clinical results of higher prothrombin levels due to the G20210A mutation using computational biology.
Here is the link (should I need it) of the FASTA for the F2 gene:
http://www.ncbi.nlm.nih.gov/nuccore/NC_000011.10?report=fasta&from=46719192&to=46739506
http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NM_000506
http://omim.org/entry/176930#0009
我在这里显然做错了什么，因为我有一个示例文档，渲染得很完美。我大约有半个小时的时间来解决这个问题，否则我会在这篇论文上得到零分。任何建议都很好。
编辑：
刚刚提交了论文。但是，我非常想知道这个问题的答案。
答案1
问题出在 \usepackage{multicols} 和 bioinfo.cls 样式表上。这会导致上述行为。删除该包（以及使用它的所有实例）即可解决问题。