| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- 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. 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 vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most 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 field 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. 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. 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.
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| 2. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 3. |
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| 4. |
- Li, Xiao, et al.
(författare)
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The A55T and K153R polymorphisms of MSTN gene are associated with the strength training-induced muscle hypertrophy among Han Chinese men.
- 2014
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Ingår i: Journal of Sports Sciences. - : Informa UK Limited. - 0264-0414 .- 1466-447X. ; 32:9, s. 883-91
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Tidskriftsartikel (refereegranskat)abstract
- Myostatin, encoded by the MSTN gene, is a strong regulator of skeletal muscle growth. The present study aimed to investigate whether the A55T and K153R polymorphisms of MSTN were associated with the strength training-induced muscle hypertrophy among Han Chinese men. A total of 94 healthy, untrained men were recruited for an 8-week strength training programme. The thicknesses of biceps and quadriceps, along with anthropometric measurements of the participants, were assessed before and after the programme. The MSTN polymorphisms were subsequently genotyped employing polymerase chain reaction-restriction fragment length polymorphism technique and confirmed by DNA sequencing. One-way analysis of variance was used to compare the pre- and post-training measurements between carriers of different polymorphic genotypes. Our results indicated that individuals with AT + TT genotype of the A55T polymorphism showed a significant increase in the thickness of biceps (0.292 ± 0.210 cm, P = 0.03), but not quadriceps (0.254 ± 0.198 cm, P = 0.07), compared to carriers of AA genotype. For the K153R polymorphism, the increases in the thicknesses of both biceps (0.300 ± 0.131 cm) and quadriceps (0.421 ± 0.281 cm) were significantly higher among individuals with KR than those with KK genotypes (P < 0.01 for both muscles). The results obtained therefore suggested a possible association between the two polymorphisms and the strength training-induced muscle hypertrophy among men of Han Chinese ethnicity.
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| 5. |
- Kyrpides, Nikos C, et al.
(författare)
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Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.
- 2014
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1545-7885. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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| 6. |
- Xu, Chun Kai, et al.
(författare)
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Nonlinear inelastic electron scattering revealed by plasmon-enhanced electron energy-loss spectroscopy
- 2014
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Ingår i: Nature Physics. - 1745-2473 .- 1745-2481. ; 10:10, s. 753-757
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Tidskriftsartikel (refereegranskat)abstract
- Electron energy-loss spectroscopy is a powerful tool for identifying the chemical composition of materials(1-5). It relies mostly on the measurement of inelastic electrons, which carry specific atomic or molecular information. Inelastic electron scattering, however, has a very low intensity, often orders of magnitude weaker than that of elastically scattered electrons. Here, we report the observation of enhanced inelastic electron scattering from silver nanostructures, the intensity of which can reach up to 60% of its elastic counterpart. A home-made scanning probe electron energy-loss spectrometer(6) was used to produce highly localized plasmonic excitations, significantly enhancing the strength of the local electric field of silver nanostructures. The intensity of inelastic electron scattering was found to increase nonlinearly with respect to the electric field generated by the tip-sample bias, providing direct evidence of nonlinear electron scattering processes.
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| 7. |
- Jiang, Wen jun, et al.
(författare)
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Adaptive Thresholding with Inverted Triangular Area for Real-Time Detection of the Heart Rate from Photoplethysmogram Traces on a Smartphone
- 2014
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Konferensbidrag (refereegranskat)abstract
- Photoplethysmogram (PPG) signals acquired by smartphone cameras are weaker than those acquired by dedicated pulse oximeters. Furthermore, the signals have lower sampling rates, have notches in the waveform and are more severely affected by baseline drift, leading to specific morphological characteristics. This paper introduces a new feature, the inverted triangular area, to address these specific characteristics. The new feature enables real-time adaptive waveform detection using an algorithm of linear time complexity. It can also recognize notches in the waveform and it is inherently robust to baseline drift. An implementation of the algorithm on Android is available for free download. We collected data from 24 volunteers and compared our algorithm in peak detection with two competing algorithms designed for PPG signals, Incremental-Merge Segmentation (IMS) and Adaptive Thresholding (ADT). A sensitivity of 98.0 % and a positive predictive value of 98.8 % were obtained, which were 7.7 % higher than the IMS algorithm in sensitivity, and 8.3 % higher than the ADT algorithm in positive predictive value. The experimental results confirmed the applicability of the proposed method.
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| 8. |
- Jiang, Wen Jun, et al.
(författare)
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Real-time Quantifying Heart Beat Rate from Facial Video Recording on a Smart Phone using Kalman Filters
- 2014
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Konferensbidrag (refereegranskat)abstract
- Photoplethysmography (PPG) can be carried out through facial video recording by a smart phone camera in ambient light. The main challenge is to eliminate motion artifacts and ambient noise. We describe a real-time algorithm to quantify the heart beat rate from facial video recording captured by the camera of a smart phone. We extract the green channel from the video. Then we normalize it and use a Kalman filter with a particular structure to eliminate ambient noise. This filter also enhances the heart pulse component in the signal distorted by Gaussian noise and white noise. After that we employ a band-pass FIR filter to remove the remaining motion artifacts. This is followed by peak detection or Lomb periodogram to estimate heart rate. The algorithm has low computational overhead, low delay and high robustness, making it suitable for real-time interaction on a smart phone. Finally we describe an Android application based on this study.
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| 9. |
- Li, Jun, et al.
(författare)
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Full-Diversity Binary Frame-Wise Network Coding for Multiple-Source Multiple-Relay Networks Over Slow-Fading Channels
- 2012
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Ingår i: IEEE Transactions on Vehicular Technology. - 0018-9545 .- 1939-9359. ; 61:3, s. 1346-1360
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Tidskriftsartikel (refereegranskat)abstract
- We study the design of network codes for M-source N-relay (M - N - 1) wireless networks over slow-fading channels. Binary frame-wise network coding (BFNC) based on cyclic-shifting matrices is developed to achieve full diversity and good coding gain. We develop a criterion in the context of BFNC that if satisfied guarantees to achieve full diversity gain. Based on this criterion, we propose an algorithm to design low-complexity encoders for a BFNC scheme by exploiting quasi-cyclic low-density parity-check (LDPC) code structures. We also design practical decoders based on the belief propagation decoding principle with a focus on large block lengths. Numerical results demonstrate that our BFNC schemes have substantial benefits over previous complex field and Galois field network coding schemes in the sense that our BFNC schemes can achieve full diversity gain and high coding gain for arbitrary block lengths with low encoding/decoding complexity.
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| 10. |
- Li, Jun, et al.
(författare)
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Threshold-Based One-Bit Soft Forwarding for a Network Coded Multi-Source Single-Relay System
- 2014
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Ingår i: IEEE Transactions on Communications. - 0090-6778 .- 1558-0857. ; 62:5, s. 1604-1620
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, we propose a threshold-based one-bit soft forwarding (TOB-SF) protocol for a multi-source relaying system with network coding, where two sources communicate with the destination with the help of a relay. Specifically in the TOB-SF protocol, the relay calculates the log-likelihood ratio (LLR) value of each network coded symbol, compares this LLR value with a pre-optimized threshold, and determines whether to transmit or keep silent. We are interested in optimizing the TOB-SF protocol in fading channels, and consider both the uncoded and low-density parity check coded systems. In the uncoded system, we first derive the bit error rate (BER) expressions at the destination, based on which, we derive the optimal threshold. Then we theoretically prove that the system can achieve the full diversity gain by using this threshold. Further, we optimize the power allocation at the relay to achieve a higher coding gain. In the coded system, we first optimize the LLR threshold. Then we develop a methodology to track the BER evolution at the destination by using Gaussian approximations. Based on the BER evolution, we further optimize the power allocation at the relay which minimizes the system BER. Simulation results show that the proposed TOB-SF protocol outperforms other conventional relaying protocols in terms of error performance.
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