Proteomics: A Paradigm Shift

ABSTRACT

Proteome—the protein complement of a genome—has become the protein renaissance and a key research tool in the post-genomic era. The basic technology involves the routine usage of gel electrophoresis and spectrometry procedures for deciphering the primary protein sequence/structure as well as knowing certain unique post-translational modifications that a particular protein has undergone to perform a specific function in the cell. However, the recent advancements in protein analysis have ushered this science to provide deeper, bigger and more valuable perspectives regarding performance of subtle protein-protein interactions. Applications of this branch of molecular biology are as vast as the subject is and include clinical diagnostics, pharmaceutical and biotechnological industries. The 21st century hails the use of products, procedures and advancements of this science as finer touches required for the grooming of fast-paced technology.     

Direct Mouse Trauma/Burn Model of Heterotopic Ossification

Heterotopic ossification (HO) is the formation of bone outside of the skeleton which forms following major trauma, burn injuries, and orthopaedic surgical procedures. The majority of animal models used to study HO rely on the application of exogenous substances, such as bone morphogenetic protein (BMP), exogenous cell constructs, or genetic mutations in BMP signaling. While these models are useful they do not accurately reproduce the inflammatory states that cause the majority of cases of HO. Here we describe a burn/tenotomy model in mice that reliably produces focused HO. This protocol involves creating a 30% total body surface area partial thickness contact burn on the dorsal skin as well as division of the Achilles tendon at its midpoint. Relying solely on traumatic injury to induce HO at a predictable location allows for time-course study of endochondral heterotopic bone formation from intrinsic physiologic processes and environment only. This method could prove instrumental in understanding the inflammatory and osteogenic pathways involved in trauma-induced HO. Furthermore, because HO develops in a predictable location and time-course in this model, it allows for research to improve early imaging strategies and treatment modalities to prevent HO formation.     

Indian Science Culture Needs a Paradigm Shift

There is a general impression in the scientific community in our country that the way science is taught, leant and the work culture of research and management of academic and research institutions is not conducive to cutting edge research, innovation and making world leaders. Mentoring continues to be poor with some exceptions. Very often, senior scientists with long innings in science teaching and research express anguish at the status quo in spite of a number of policy documents and recommendations for change. Indian science culture (teaching, research as well as administration) is a matter of prime concern and the issues cannot be pushed under the carpet if we desire a qualitative change. Most of the institutions of higher learning churn out graduates and post graduates who are largely unemployable. There are concerns on the number of Ph.Ds and not on the quality of Ph.D. One major consequence of the weak post graduates and Ph.Ds is the non-availability of competent faculty. Weakness and lack of interest in science learning starts from school. Learning continues to be by rote which is the prime reason for our low global rank in science and mathematics competence. Teaching and research apart there are umpteen other issues in over all culture of institutions and universities engaged in science teaching and research. Few oases of excellence are exceptions in the vast pool of mediocrity. Some points which need prime attention are: adoption of a tenure track system on the pattern of US institutions; feedback on and evaluation of teaching and mentoring; bottom up approach for candid feedback on issues which require long term solutions for efficiency and sound deliverables, cultivating the culture of working in front line areas, full transparency in working and an all out exit from culture of feudalism. This transformation needs commitment on the part of the politicians who man the respective departments of science education, research and human resource development. I am sure such a cultural change and paradigm shift from the status quo does not need extra funds and can be surely ushered in without money.     

Spatiotemporal Characterization of a Fibrin Clot Using Quantitative Phase Imaging

Studying the dynamics of fibrin clot formation and its morphology is an important problem in biology and has significant impact for several scientific and clinical applications. We present a label-free technique based on quantitative phase imaging to address this problem. Using quantitative phase information, we characterized fibrin polymerization in real-time and present a mathematical model describing the transition from liquid to gel state. By exploiting the inherent optical sectioning capability of our instrument, we measured the three-dimensional structure of the fibrin clot. From this data, we evaluated the fractal nature of the fibrin network and extracted the fractal dimension. Our non-invasive and speckle-free approach analyzes the clotting process without the need for external contrast agents.     

Brain Characterization Using Normalized Quantitative Magnetic Resonance Imaging

Objectives

To present a method for generating reference maps of typical brain characteristics of groups of subjects using a novel combination of rapid quantitative Magnetic Resonance Imaging (qMRI) and brain normalization. The reference maps can be used to detect significant tissue differences in patients, both locally and globally.

Materials and Methods

A rapid qMRI method was used to obtain the longitudinal relaxation rate (R₁), the transverse relaxation rate (R₂) and the proton density (PD). These three tissue properties were measured in the brains of 32 healthy subjects and in one patient diagnosed with Multiple Sclerosis (MS). The maps were normalized to a standard brain template using a linear affine registration. The differences of the mean value ofR₁, R₂ and PD of 31 healthy subjects in comparison to the oldest healthy subject and in comparison to an MS patient were calculated. Larger anatomical structures were characterized using a standard atlas. The vector sum of the normalized differences was used to show significant tissue differences.

Results

The coefficient of variation of the reference maps was high at the edges of the brain and the ventricles, moderate in the cortical grey matter and low in white matter and the deep grey matter structures. The elderly subject mainly showed significantly lower R₁ and R₂ and higher PD values along all sulci. The MS patient showed significantly lower R₁ and R₂ and higher PD values at the edges of the ventricular system as well as throughout the periventricular white matter, at the internal and external capsules and at each of the MS lesions.

Conclusion

Brain normalization of rapid qMRI is a promising new method to generate reference maps of typical brain characteristics and to automatically detect deviating tissue properties in the brain.     

Evidence for a Regime Shift in Nitrogen Export from a Forested Watershed

In this study, we document a functional regime shift in stream inorganic nitrogen (N) processing indicated by a major change in N export from a forested watershed. Evidence from 36 years of data following experimental clearcut logging at Coweeta Hydrologic Laboratory, NC, suggests that forest disturbance in this area can cause elevation of dissolved inorganic N (DIN) loss lasting decades or perhaps longer. This elevation of N export was apparently caused by an initial pulse of organic matter input, reduced vegetation uptake, increased mineralization of soil organic N, and N fixation by black locust-associated bacteria following clearcut logging. In forested reference watersheds at Coweeta, maximum DIN concentration occurs in summer when base flow is low, but the clearcut watershed shifted to a pattern of maximum winter DIN concentration. The seasonal pattern of DIN concentration and export from reference watersheds can be explained by terrestrial and in-stream processes, but following clearcutting, elevated DIN availability saturated both terrestrial and in-stream uptake, and the N export regime became dominated by hydrologic transport. We suggest that the long-term elevation of stream DIN concentration and export along with the changes in seasonality of DIN export and the relationship between concentration and discharge represent a functional regime shift initiated by forest disturbance.     

Plant Neurobiology as a Paradigm Shift Not Only in the Plant Sciences

Plants are complex living beings, extremely sensitive to environmental factors, continuously adapting to the ever changing environment. Emerging research document that plants sense, memorize, and process experiences and use this information for their adaptive behavior and evolution. As any other living and evolving systems, plants act as knowledge accumulating systems. Neuronal informational systems are behind this concept of organisms as knowledge accumulating systems because they allow the most rapid and efficient adaptive responses to changes in environment. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants. The journal, Plant Signaling & Behavior, was launched as a platform for exchanging information and fostering research on plant neurobiology in order to allow our understanding of plants in their whole integrated, communicative, and behavioral complexity.

I always go by official statistics because they are very carefully compounded and, even if they are false, we have no others …∼ Jaroslav Hašek, 1911

Key Words: plant neurobiology, sensory biology, behavior, biological complexity, evolution, signal integrationThis quotation of writer and mystificator Jaroslav Hašek is from his electorial speech aimed to get a seat in the Austro-Hungarian parliament for his imaginary political party ‘Moderate Progress within the Limits of the Law’ in 1911. It indicates how statistics can be misused for manipulation of public opinion, sometimes allegedly for general good. This quotation is partially relevant also for recent biology which is passing through a critical cross-road from reductionist-mechanistic concepts and methodologies towards the post-genomic, holistic, systems-based analysis of integrated and communicative hierarchic networks known as life processes.There is a message hidden in this Hašek''s aphorism. All those mathematical models, scientific theories and concepts, however appealing, harmonious and long-standing … but which do not correspond to reality …; inevitably will be ‘killed by ugly’ facts generated by scientific progress, and finally replaced by new models, theories, and concepts.¹Despite the indisputable success of the reductionistic approach in providing many discoveries regarding single cells and their components, it is increasingly clear that promises of ‘mechanistic’ genocentric biology were just chimeras and that living organisms are much more complex than the sum of their constituents. Ernst Mayr, in his final opus, almost a testament published at his age of 100, strongly opposed the belief that the reductionism at the molecular level could help to explain the complexity of life. He stressed that the concept of biological “emergence”, which deals with the occurrence of unexpected features in complex living systems, is not fully accessible using only physical and chemical approaches.²Themes of hierarchy, continuity, and order dominated biology before the turn of the century, but these have in many cases been replaced by images of the workshop. Examples include such terms as ‘machineries’, ‘mechanistic understanding’, ‘mechanistic explanation’, ‘motors’, ‘machines’, ‘clocks’ etc. This shift may well reflect the characteristic style of our age. These concepts, although useful for mining of details, do not reveal the true complexity of life and can be misleading. Even a one-celled organism is made up of ‘millions’ of subcellular parts. Concerning the great complexity of unicellular creatures Ilya Prigogine (1973) wrote: “… but let us have no illusions, our research would still leave us quite unable to grasp the extreme complexity of the simplest of organism.”³ Moreover, eukaryotic cell proved to be, in fact, ‘cells within cell’,^4–8 while there are numerous supracellular situations, the most dramatic one is represented by plants when all cells are interconnected via plasmodesmata into supracellular organism.⁶ All this collectively indicate that the currently valid ‘Cell Theory’ dogma is approaching its replacement with a new updated concept of a basic unit of eukaryotic life.^6–8All those mathematical models, scientific theories and concepts, however appealing, harmonious and long-standing … but which do not correspond to reality …; inevitably will be ‘killed by ugly’ facts generated by scientific progress, and finally replaced by new models, theories, and concepts.Furthermore, genomes are much more complex and dynamic as we ever anticipated.^9,10 They often have as much as 99% of non-coding DNA sequences,¹¹ which is not ‘junk DNA’ but rather DNA which is part of multitask networks integrating coding DNA.¹² In genomes exposed to stress (like mutations), changes are scored preferentially in non-coding sequences which regain a new balance by complex changes in genome composition and activity.^9,10,13,14 There are several definitions regarding what is gene¹¹ and molecular biologists and genetics are learning to be careful not to make strong conclusions from under-expression, knocking-out, or overexpression of any particular gene. It is increasingly clear that mutations in single genes are accompanied with altered expressions of other genes and non-coding DNA sequences too, and even subtle re-arrangements of chromatin structure and genome architecture are possible. The dynamic genome actively regains the lost balance, also via extensive re-shufflings of non-coding DNA.After complete sequencing of numerous genomes, it is clear that our understanding of what constitutes life and what distinguishes living biological systems from non-living chemical - biochemical systems is not much better than our understanding before the start of the genomics era some 60 years ago. Yet, it is also obvious that living systems, whether single cells or whole complex organisms like animals and plants, are not machines and automata which respond to external signals via a limited set of predefined responses and automatic reflexes. While humans and other animals, even insects, are already out of this ‘mechanistic’ trap^15,16 which can be traced back to Descartes,¹⁷ plants are still considered to act only in predetermined automatic fashions, as mechanical devices devoid of any possibility for choice and planning of their activities. In contrast to machines, life systems are based on wet chemistry, being systems of hierarchical and dynamic integration, communication and emergence.^1,18Recently, a critical mass of data has accumulated demanding reconsideration of this mechanistic view of plants.^19,20 Plants are complex living beings, extremely sensitive to environmental factors and continuously adapting to the ever changing environment.²¹ In addition, plants respond to environmental stimuli as integrated organisms. Often, plants make important decisions, such as onset or breakage of dormancy and onset of flowering, which implicate some central or decentralized command center. Moreover, roots and shoots act in an integrated manner allowing dynamic balance of above-ground and below-ground organs. The journal, Plant Signaling & Behavior, was launched as a platform for exchange of information about the integration of discrete processes, including subcellular signalling integrated with higher-level processes. Signal integration and communication results in adaptive behavior of whole supracellular organisms, encompassing also complex, and still elusive, plant-plant, plant-insect, and plant-animal communications. Coordinated behavior based on sensory perception is inherent for neurobiological systems.²² Therefore, plants can be considered for neuronal individuals. Moreover, plants are also able to share knowledge perceived from environment with other plants, communicating both private and public messages.^23,24 This implicates social learning and behavioral inheritance in plants too.After complete sequencing of numerous genomes, it is clear that our understanding of what constitutes life and what distinguishes living biological systems from non-living chemical - biochemical systems is not much better than our understanding before the start of genomics era some 60 years ago.

Behavior

1. An activity of a defined organism: observable activity when measurable in terms of quantitative effects of the environment whether arising from internal or external stimuli.
2. Anything that an organism does that involves action and response to stimulation.

(Webster Third New International Dictionary 1961).Neuronal informational systems allow the most rapid and efficient adaptive responses. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants.Some of our colleagues assert that plants do not exhibit any integrated neuronal principles.²⁵ They maintain that plants do not show complex experience- or learning-based behavior. Plants, they aver, act rather as machines manifesting predefined reflexes. Yet recent studies indicate that even prokaryotic bacteria exhibit cognitive behavior^26,27 and posses linguistic communication and rudimentary intelligence.^28–30 Therefore, it should not be too surprising that plants also show features of communication and even plant-specific cognition.^{19,20,31,32–35} As any other living systems, plants act as ‘knowledge accumulating systems’.¹ In fact, in order to adapt, all organisms continuously generate hypotheses about their environment via well formulated ‘questions’ which are solved by an increasing set of possible ‘answers’ in order to adapt.¹ Neuronal informational systems are behind this concept of organisms as ‘knowledge accumulating systems’ because they allow the most rapid and efficient adaptive responses.²² As a consequence, neuronal computation is not limited to animal brains but is used also by bacteria and plants.Reductionistic approaches will continue to “atomize” biological systems. Nevertheless, the avalanche of new data will be in need of functional integration, winning adherents to the idea that plants have integrated signaling and communicative systems that endowed them with complex and adaptive behavior. We trust that Plant Signaling & Behavior, will become an important platform for exchange of these ideas. With progress of sciences, plants show more and more similarities to animals despite obviously plant-specific evolutionary origins, cellular basis, and multicellularity. We can just mention sexuality and sex organs, embryos, stem cells, immunity, circadian rhythms, hormonal and peptide signaling, sensory perception and bioelectricity including action potentials, communication and neurobiological aspects of signal integration. The whole picture strongly suggest that convergent evolution is much more important^36,37 than currently envisioned in evolutionary theories.Reductionistic approaches will continue to “atomize” biological systems. Nevertheless, the avalanche of new data will be in need of functional integration, winning adherents to the idea that plants have integrated signaling and communicative systems that endowed them with complex and adaptive behavior.We have started with Jaroslav Hašek and we close with him as well. His quotation from 1911 is also a warning for future that we should stay open-minded. We should not slip into dogmatic ‘traps’ which have been so characteristic for the mechanistic and genocentric biology. Mathematics and computational biology are important tools, and surely will play decisive role in systems biology in the future. But they can be easily misinterpreted, and even misused. Plant systems biology, and the whole biology in general, must overcome dogmas of mechanistic genocentric biology. We hope that characterizing plants in their whole behavioral and communicative complexity will allow us to better understand what is life and how it emerged from chemical and biochemical complex systems.     

Reinventing the Museum: Historical and Contemporary Perspectives on the Paradigm Shift

Reinventing the Museum: Historical and Contemporary Perspectives on the Paradigm Shift . Gail Anderson, ed. Marburg an der Lahn: Basilisken Press, 2004. 401 pp.     

外固定支架及开放手术治疗肘关节严重异位骨化疗效分析

目的:探讨外固定支架及开放手术治疗治疗肘关节严重异位骨化的方法及疗效。方法:自2007年9月至2012年9月,对18例(其中男13例女5例,平均年龄33.5岁)创伤后严重异位骨化性肘关节僵硬患者进行开放手术及外固定支架治疗。所有患者均采用相同的手术方式,即取出原有内固定,前置尺神经,松解关节囊粘连,清除异位骨化。对患者肘关节屈伸范围术前及术后均评估,采用Mayo肘关节评分肘关节功能(MEPI)评估疗效。术后予以指导康复锻炼。结果:术后患者的屈伸分别平均增加到125°和10°,MEPI评分由术前的平均50分提高到术后的90分。结论:外固定支架及开放手术治疗治疗严重异位骨化性肘关节僵硬具有确切的疗效。     

Heterotopic transplantation in the syncytial blastoderm ofDrosophila: Evidence for anterior and posterior nuclear commitments

Summary The interaction ofDrosophila syncytial blastoderm nuclei and cortical cytoplasm in the control of somatic developmental commitments was studied by transplanting genetically marked nuclei and surrounding cytoplasm between anterior and posterior flanks. After completion of cellularization the host egg was cut. Host anterior or posterior partial embryos were cultured in adult abdomens for 8–10 days, then the larval tissue removed and injected into larval hosts for metamorphosis. Differentiated ectodermal implants were recovered from emerged adults and characterized. One hundred sixteen clearly interpretable control and experimental implants were found. Of the 73 experimental implants 15 were derived from donor nuclei.Among the 15 donor implants, 14 autonomously formed donor site anterior (head and thoracic) or posterior (abdomen and genital) structures. This donor autonomy is interpreted to mean that nuclear and cytoplasmic factors necessary for anterior and posterior somatic commitments are present and transplantable prior to the completion of cellularization. Since donor nuclei injected directly into host flanks, or premixed with host cytoplasm, would have been well exposed to any host cytoplasmic factors, donor nuclei appear to have adopted anterior or posterior somatic commitments which are stable to significant cytoplasmic alterations.In 14 implants, host nuclei exposed to donor material altered somatic fate and formed donor type structures. These conversions are interpreted to imply that cytoplasmic factors controlling anterior or posterior somatic fates are present in the syncytial balstoderm embryo.     

胶原诱导型关节炎大鼠的关节影像学特点

目的旨在分析CIA X线片四肢关节的破坏特点,揭示CIA大鼠关节破坏的规律,为规范评分方案提供依据。方法采用П型胶原和弗氏完全佐剂皮下注射清洁级Wistar大鼠,造模成功（每批10只,共3次）后第35天行全身X线钼靶照片,以正常组作为对照、每只大鼠评价96块骨破坏（erosion）和100个关节间隙（joint space narrowing,JSN）;处死动物,取左前肢和右后肢近端第3足趾关节苏木素-伊红（HE）染色,评价中性粒细胞、淋巴细胞、浆细胞浸润、滑膜增生和软骨破坏的情况。结果造模成功后CIA大鼠关节出现明显的红肿,活动受限;HE病理显示,CIA关节存在明显的中性粒细胞、淋巴细胞和浆细胞浸润,滑膜增生,纤维组织增生,软骨破坏;X线片分析结果显示：①广泛性骨质疏松,边缘性骨质侵蚀,关节间隙狭窄或增宽,部分踝关节间隙消失,关节相互融合甚至骨性强直。②67%的骨出现erosion,JSN影响为78%,关节破坏以中、重度为主;③远端、近端趾间关节和踝关节发病率高,损害严重,掌趾关节发病率低,破坏较轻。④后肢关节破坏重于前肢（P〈0.01）,左右肢没有显著性差异（P〉0.05）。结论①滑膜是CIA炎症反应启动的主要病灶,与骨交界的滑膜和血管翳造成了CIA的骨质破坏;②CIA影像学表现关节破坏严重,以远端、近端趾间关节和踝关节为主,这些关节可作为评价破坏程度的选择。本研究对于深入CIA关节破坏的病因病理和进一步规范X线片评分方案具有一定意义。     

Characterization of Breast Tumors Using Diffusion Kurtosis Imaging (DKI)

Aim

The aim of this study was to investigate and evaluate the role of magnetic resonance (MR) diffusion kurtosis imaging (DKI) in characterizing breast lesions.

Materials and Methods

One hundred and twenty-four lesions in 103 patients (mean age: 57±14 years) were evaluated by MR DKI performed with 7 b-values of 0, 250, 500, 750, 1,000, 1,500, 2,000 s/mm² and dynamic contrast-enhanced (DCE) MR imaging. Breast lesions were histologically characterized and DKI related parameters—mean diffusivity (MD) and mean kurtosis (MK)—were measured. The MD and MK in normal fibroglandular breast tissue, benign and malignant lesions were compared by One-way analysis of variance (ANOVA) with Tukey''s multiple comparison test. Receiver operating characteristic (ROC) analysis was performed to assess the sensitivity and specificity of MD and MK in the diagnosis of breast lesions.

Results

The benign lesions (n = 42) and malignant lesions (n = 82) had mean diameters of 11.4±3.4 mm and 35.8±20.1 mm, respectively. The MK for malignant lesions (0.88±0.17) was significantly higher than that for benign lesions (0.47±0.14) (P<0.001), and, in contrast, MD for benign lesions (1.97±0.35 (10⁻³ mm²/s)) was higher than that for malignant lesions (1.20±0.31 (10⁻³ mm²/s)) (P<0.001). At a cutoff MD/MK 1.58 (10⁻³ mm²/s)/0.69, sensitivity and specificity of MD/MK for the diagnosis of malignant were 79.3%/84.2% and 92.9%/92.9%, respectively. The area under the curve (AUC) is 0.86/0.92 for MD/MK.

Conclusions

DKI could provide valuable information on the diffusion properties related to tumor microenvironment and increase diagnostic confidence of breast tumors.     

Transplantation of Pulmonary Valve Using a Mouse Model of Heterotopic Heart Transplantation

Tissue engineered heart valves, especially decellularized valves, are starting to gain momentum in clinical use of reconstructive surgery with mixed results. However, the cellular and molecular mechanisms of the neotissue development, valve thickening, and stenosis development are not researched extensively. To answer the above questions, we developed a murine heterotopic heart valve transplantation model. A heart valve was harvested from a valve donor mouse and transplanted to a heart donor mouse. The heart with a new valve was transplanted heterotopically to a recipient mouse. The transplanted heart showed its own heartbeat, independent of the recipient’s heartbeat. The blood flow was quantified using a high frequency ultrasound system with a pulsed wave Doppler. The flow through the implanted pulmonary valve showed forward flow with minimal regurgitation and the peak flow was close to 100 mm/sec. This murine model of heart valve transplantation is highly versatile, so it can be modified and adapted to provide different hemodynamic environments and/or can be used with various transgenic mice to study neotissue development in a tissue engineered heart valve.