Clusters Of Sites Research Articles

Whole-genome landscape of adult T-cell leukemia/lymphoma

AbstractAdult T-cell leukemia/lymphoma (ATL) is an aggressive neoplasm immunophenotypically resembling regulatory T cells, associated with human T-cell leukemia virus type-1. Here, we performed whole-genome sequencing (WGS) of 150 ATL cases to reveal the overarching landscape of genetic alterations in ATL. We discovered frequent (33%) loss-of-function alterations preferentially targeting the CIC long isoform, which were overlooked by previous exome-centric studies of various cancer types. Long but not short isoform–specific inactivation of Cic selectively increased CD4+CD25+Foxp3+ T cells in vivo. We also found recurrent (13%) 3′-truncations of REL, which induce transcriptional upregulation and generate gain-of-function proteins. More importantly, REL truncations are also common in diffuse large B-cell lymphoma, especially in germinal center B-cell–like subtype (12%). In the non-coding genome, we identified recurrent mutations in regulatory elements, particularly splice sites, of several driver genes. In addition, we characterized the different mutational processes operative in clustered hypermutation sites within and outside immunoglobulin/T-cell receptor genes and identified the mutational enrichment at the binding sites of host and viral transcription factors, suggesting their activities in ATL. By combining the analyses for coding and noncoding mutations, structural variations, and copy number alterations, we discovered 56 recurrently altered driver genes, including 11 novel ones. Finally, ATL cases were classified into 2 molecular groups with distinct clinical and genetic characteristics based on the driver alteration profile. Our findings not only help to improve diagnostic and therapeutic strategies in ATL, but also provide insights into T-cell biology and have implications for genome-wide cancer driver discovery.

Characterization and Application of a New β-Galactosidase Gal42 From Marine Bacterium Bacillus sp. BY02.

β-Galactosidase plays an important role in medicine and dairy industry. In this study, a new glycoside hydrolase family 42 (GH42) β-galactosidase-encoding gene, gal42, was cloned from a newly isolated marine bacterium Bacillus sp. BY02 and expressed in Escherichia coli. Structural characterization indicated that the encoding β-galactosidase, Gal42, is a homotrimer in solution, and homology modeling indicated that it retains the zinc binding sites of the Cys cluster. The reaction activity of Gal42 was significantly increased by Zn2+ (229.6%) and other divalent metal ions (Mn2+, Mg2+, and Co2+), while its activity was inhibited by EDTA (53.9%). Meanwhile, the thermo-stability of the Gal42 was also significantly enhanced by 5 and 10 mM of zinc ion supplement, which suggested that the “Cys-Zn” motif played important roles in both structural stability and catalytic function. Furthermore, Gal42 showed effective lactose hydrolysis activity, which makes the enzyme hydrolyze the lactose in milk effectively. These properties make Gal42 a potential candidate in food technology.

Machine learning dynamic correlation in chemical kinetics.

Lattice models are a useful tool to simulate the kinetics of surface reactions. Since it is expensive to propagate the probabilities of the entire lattice configurations, it is practical to consider the occupation probabilities of a typical site or a cluster of sites instead. This amounts to a moment closure approximation of the chemical master equation. Unfortunately, simple closures, such as the mean-field and the pair approximation (PA), exhibit weaknesses in systems with significant long-range correlation. In this paper, we show that machine learning (ML) can be used to construct accurate moment closures in chemical kinetics using the lattice Lotka-Volterra model as a model system. We trained feedforward neural networks on kinetic Monte Carlo (KMC) results at select values of rate constants and initial conditions. Given the same level of input as PA, the ML moment closure (MLMC) gave accurate predictions of the instantaneous three-site occupation probabilities. Solving the kinetic equations in conjunction with MLMC gave drastic improvements in the simulated dynamics and descriptions of the dynamical regimes throughout the parameter space. In this way, MLMC is a promising tool to interpolate KMC simulations or construct pretrained closures that would enable researchers to extract useful insight at a fraction of the computational cost.

The Influence of UiO‐bpy Skeleton for the Direct Methane‐to‐Methanol Conversion on Cu@UiO‐bpy: Importance of the Encapsulation Effect

AbstractThe influence of UiO‐bpy skeleton for the direct methane‐to‐methanol conversion on Cu@UiO‐bpy is studied by experiment and DFT. It is found that Cu@UiO‐bpy shows high methanol yield and stability. However, if the UiO‐bpy skeleton is destroyed, the active sites of small CuxOx clusters grow into CuO nanoparticles due to the thermal movement during the reaction. As a result, the catalyst is deactivated. In other words, the encapsulation effect is a key factor for catalyst stability, which prevents the growth of CuxOx clusters. In addition, the encapsulation effect of UiO‐bpy skeleton affects the morphology and size of CuxOx clusters, of which small CuxOx clusters are beneficial for methane conversion.

Spectral properties of strongly correlated multi-impurity models in the Kondo insulator regime: Emergent coherence, metallic surface states, and quantum phase transitions

We investigate the real-space spectral properties of strongly-correlated multi-impurity arrays in the Kondo insulator regime. Employing a recently developed mapping onto an effective correlated cluster problem makes the problem accessible to the numerical renormalization group. The evolution of the spectrum as function of cluster size and cluster site is studied. We applied the extended Lieb-Mattis theorem to predict whether the spectral function must vanish at the Fermi energy developing a true pseudo-gap or whether the spectral function remains finite at $\w=0$. Our numerical renormalization group spectra confirm the predictions of the theorem and shows a metallic behavior at the surface of a cluster prevailing in arbitrary spatial dimensions. We present a conventional minimal extension of a particle-hole symmetric Anderson lattice model at $U=0$ that leads to a gapped bulk band but a surface band with mainly $f$-orbital character for weak and moderate hybridization strength. The change in the site-dependent spectra upon introducing a Kondo hole in the center of the cluster are presented as a function of the hole-orbital energy. In particular the spectral signatures across the Kosterlitz-Thouless type quantum phase transition from a singlet to a local moment fixed point are discussed.

Application of Fossil and Artefact Collection in The Human Reservation Center Sangiran of Sragen Krikilan Cluster Based on Android

Sangiran is the biggest early man site in Indonesia which has an important value such as human evolutions, culture, early fauna, and its environments. The evidence of the living past of early man sees through fossil collection, artifact, and environment. Sangiran collections save in Sangiran Early man Museum, under the management of the Preservation Center of Early Man Site Sangiran. Sangiran site is recognized as a World Cultural Heritage that has a problem in disseminating information about its important value. There are still many people who don't know about the important value of Sangiran.
 The result of the research, the writer makes a mobile informative system that is "Application of the Introduction of Fossil and Artefact Collection in the Preservation Center of Early Man Sangiran Site Cluster Krikilan Based on Android". The advantage of this system is it can be an introduction media by the Preservation Center of Early Man Site Sangiran which only used with Android, meanwhile the weakness is it can only be operated on Android, not yet able to iOS and desktop.

Analysing the impact of electrification on rural attractiveness in Senegal with mobile phone data.

Reliable and affordable access to electricity has become one of the basic needs for humans and is, as such, at the top of the development agenda. It contributes to socio-economic development by transforming the whole spectrum of people’s lives—food, education, healthcare. It spurs new economic opportunities, thus improving livelihoods. Using a comprehensive dataset of pseudonymized mobile phone records, we analyse the impact of electrification on attractiveness for rural areas in Senegal. We extract communication and mobility flows from call detail records and show that electrification is positively and specifically correlated with centrality measures within the communication network and with the volume of incoming visitors. This increased influence is however circumscribed to a limited spatial extent, creating a complex competition with nearby areas. Nevertheless, we found that the volume of visitors between any two sites could be well predicted from the level of electrification at the destination and the living standard at the origin. In view of these results, we discuss how to obtain the best outcomes from a rural electrification planning strategy. We determine that electrifying clusters of rural sites is a better solution than centralizing electricity supplies to maximize the development of specifically targeted sites.

Ru clusters confined in Hydrogen-bonded organic frameworks for homogeneous catalytic hydrogenation of N-heterocyclic compounds with heterogeneous recyclability

Combining the advantages of homogeneous catalysis and the recyclability of heterogeneous catalysts is highly desired for sustainable catalysis but remains a challenging goal. In the current work, hydrogen-bonded organic frameworks (HOFs) that consist of cage molecules with amino groups were prepared. The HOFs with heteroatom-containing porous cavities and stable backbone confine ultrafine Ru clusters with diameter of about 0.47 nm and high Ru loading of 30 wt%. The obtained Ru@HOF catalyst can well disperse in water in the form of discrete cage-confined Ru clusters similar to a homogeneous catalyst, and can be recycled easily through simple precipitation by the addition of acetone due to the formation of hydrogen bonds between discrete cages. The Ru@HOF was used as a homogenous catalyst for efficiently selective catalytic hydrogenation of N-heteroarene compounds, such as quinolines and indoles in aqueous solution. Especially quinoline compounds can be fully hydrogenated to decahydroquinoline with Ru@HOF catalyst, which is not easy to be implemented with other Ru nanoparticle-based catalysts. The high catalytic performance of Ru@HOF is attributed to the homogeneously dispersed and accessible active sites of the ultrafine Ru clusters. This study provides a novel strategy for fabricating ultrafine noble metal clusters-based catalysts with homogeneous catalytic performance and heterogeneous recyclability.

Core-Doped [(Cd1-xCox)10S4(SPh)16]4- Clusters from a Self-Assembly Route.

The incorporation of substitutional Co2+ impurities in [Cd10S4(SPh)16]4- (Cd10) molecular clusters prepared by the self-assembly method where Na2S is the sulfur precursor and a redox method where elemental S is the sulfur precursor is studied. The Co2+ ions provide unique spectroscopic and chemical handles to monitor dopant speciation during cluster formation and determine what role, if any, other cluster species play during Cd10 cluster formation. In contrast to the redox method that produces exclusively surface-exchanged Co2+-doped Cd10 (Co:Cd10), the preparation of Cd10 by the self-assembly method in the presence of Co2+ ions results in Co2+ incorporation at both the surface and core sites of the Cd10 cluster. Electrospray ionization mass spectrometry (ESI-MS) analysis of the dopant distribution for the self-assembly synthesis of Co:Cd10 is consistent with a near-Poissonian distribution for all nominal dopant concentrations albeit with reduced actual Co2+ incorporation. At a nominal Co2+ concentration of 50%, we observe incorporation of up to seven Co2+ ions within the Cd10 self-assembled cluster compared to a maximum of only four Co2+ dopants in the Cd10 redox clusters. The observation of up to seven Co2+ dopants must involve substitution of at least three core sites within the Cd10 cluster. Electronic absorption spectra of the Co2+ ligand field transition in the heavily doped Co:Cd10 clusters display clear deviation with the surface-doped Co2+-doped Cd10 clusters prepared by the redox method. We hypothesize that the coordination of Co2+ and S2- ions in solution prior to cluster formation, which is possible only with the self-assembly method, is critical to the doping of Co2+ ions within the Cd10 cores.

Machine learning clustering and classification of human microbiome source body sites

Distinct microbial signatures associated with specific human body sites can play a role in the identification of biological materials recovered from the crime scene, but at present, methods that have capability to predict origin of biological materials based on such signatures are limited. Metagenomic sequencing and machine learning (ML) offer a promising enhancement to current identification protocols. We use ML for forensic source body site identification using shotgun metagenomic sequenced data to verify the presence of microbiomic signatures capable of discriminating between source body sites and then show that accurate prediction is possible. The consistency between cluster membership and actual source body site (purity) exceeded 99% at the genus taxonomy using off-the-shelf ML clustering algorithms. Similar results were obtained at the family level. Accurate predictions were observed for genus, family, and order taxonomies, as well as with a core set of 51 genera. The accurate outcomes from our replicable process should encourage forensic scientists to seriously consider integrating ML predictors into their source body site identification protocols.

Engineering Escherichia coli for high-yield production of ectoine

Ectoine is a natural macromolecule protector and synthesized by some extremophiles. It provides protections against radiation-mediated oxidative damages and is widely used as a bioactive ingredient in pharmaceutics and cosmetics. To meet its growing commercial demands, we engineered Escherichia coli strains for the high-yield production of ectoine. The ectABC gene cluster from the native ectoine producer Halomonas elongata was introduced into different Escherichia coli (E. Coil) strains via plasmids and 0.8 g L-1 of ectoine was produced in flask cultures by engineered E. coli BL21 (DE3). Subsequently, we designed the ribosome-binding sites of the gene cluster to fine-tune the expressions of genes ectA, ectB, and ectC, which increased the ectoine yield to 1.6 g L-1. After further combinatorial overexpression of Corynebacterium glutamicum aspartate kinase mutant (G1A, C932T) and the H. elongate aspartate-semialdehyde dehydrogenase to increase the supply of the precursor, the titer of ectoine reached to 5.5 g L-1 in flask cultures. Finally, the engineered strain produced 60.7 g L-1 ectoine in fed-batch cultures with a conversion rate of 0.25 g/g glucose.

Rice Yield Simulation and Planting Suitability Environment Pattern Recognition at a Fine Scale

Analyzing rice yields and multidimensional environmental factors at a fine scale facilitates the discovery of the planting environment patterns that guide the spatial layout of rice production. This study uses Pucheng County, Fujian Province, a demonstration county of China Good Grains and Oils, as the research area. Using actual rice yield sample data and environment data, a yield simulation model based on random forest regression is constructed to realize a fine-scale simulation of rice yield and its spatial distribution pattern in Pucheng County. On this basis, we construct a method system to identify spatial combination patterns between rice yields and fine-scale multidimensional environmental planting suitability using rice yield data and environmental planting suitability evaluation data. We categorize the areas into four combination model areas to analyze the spatial correlation model of planting suitability, multidimensional environment, and yield: higher-yield and higher-suitability cluster–comprehensive environmental-advantage areas, high-yield and high-suitability cluster–soil condition-limited areas, moderate-yield and moderate-suitability cluster–irrigation and drainage condition-limited areas, and low-yield and low-suitability cluster–site condition-limited areas. The following results are found. (1) The rice yield simulation model, which is based on random forest regression, considers the various complex relationships between yield and natural as well as human factors to realize the refined simulation of rice yields at a county scale. (2) The county rice yield has a strong positive spatial correlation, and the spatial clustering characteristics are obvious; these relationships can provide a basis for effectively implementing intensive rice planting in Pucheng County. (3) We construct a spatial combination pattern recognition method based on rice yield and environmental planting suitability. We can use this method to effectively identify the spatial relationship between yield and planting suitability as well as the shortcomings and advantages of different regions in terms of the climate, soil, irrigation, site, mechanical farming, and similar factors. On this basis, we can provide regional rice planting guidance for Pucheng County. In addition, this method system also provides a new perspective and method for research into spatial combination models and related spatial issues.

EFFECT SIZE–DRIVEN SAMPLE-SIZE PLANNING, RANDOMIZATION, AND MULTISITE USE IN L2 INSTRUCTED VOCABULARY ACQUISITION EXPERIMENTAL SAMPLES

AbstractIn this focused methodological synthesis, the sample construction procedures of 110 second language (L2) instructed vocabulary interventions were assessed in relation to effect size–driven sample-size planning, randomization, and multisite usage. These three areas were investigated because inferential testing makes better generalizations when researchers consider them during the sample construction process. Only nine reports used effect sizes to plan or justify sample sizes in any fashion, with only one engaging in an a priori power procedure referencing vocabulary-centric effect sizes from previous research. Randomized assignment was observed in 56% of the reports while no report involved randomized sampling. Approximately 15% of the samples observed were constructed from multiple sites and none of these empirically investigated the effect of site clustering. Leveraging the synthesized findings, we conclude by offering suggestions for future L2 instructed vocabulary researchers to consider a priori effect size–driven sample planning processes, randomization, and multisite usage when constructing samples.

Subnano-FeOx Clusters Anchored in an Ultrathin Amorphous Al2O3 Nanosheet for Styrene Epoxidation

The development of low-cost, high-performance catalysts at the atomic level has drawn scientists’ attention due to the high atom efficiency, unique structure, and potentially high catalytic selectivity. Among the atomically tailored catalysts, nanoclusters are of particular interest because they represent an underexplored medium state between isolated single atoms and typical nanoparticles. In this study, we report a wet-chemistry approach to synthesize highly dispersed subnano-FeOx clusters anchored on an ultrathin amorphous Al2O3 nanosheet (or Al2O3–FeOx nanosheet) and its excellent catalytic performance for selective conversion of styrene to styrene oxide. The reasons for the high catalytic performance of the Al2O3–FeOx nanosheet are 2-fold. One is that the unsaturated and amorphous nature of the Fe atoms in the subnano-FeOx clusters promotes the adsorption of styrene onto the catalytic sites of FeOx clusters for epoxidation. The other is that the amorphous Al2O3 nanosheet prevents the aggregation of catalytic FeOx clusters during the epoxidation reaction because its defective structure immobilizes the FeOx clusters.

Regional development: organizational and economic mechanism in the context of the fourth industrial revolution

Relevance of the research topic. The information and knowledge flow management is an important component for regional development in the context of the fourth industrial revolution. It allows taking advantage of the opportunities hidden in the digital transformation of the business community and providing the transformations necessary to reorient development towards inclusive and sustainable growth. Formulation of the problem. Managing the process of introducing Industry 4.0 technologies based on effective state and collective strategies opens up opportunities for regional development, but requires the development of special decision support tools, scientific substantiation of the model of systemic transformation of the region, identification of the main stakeholders and the mechanism of their interaction. Analysis of recent research and publications. The works of such researchers as Yasheva G. A. and Fateev V. S. (Belarus), Lenchuk E. B. (Russia), Götz M. and Jankowska B. (Poland), Ciffolilli A. and Muscio A. (Italy) and others are devoted to the issues of territorial and regional development in the context of the fourth industrial revolution. Selection of unexplored parts of the general problem. The mechanism of small businesses involving in the process of the necessary systemic transformation in the context of the fourth industrial revolution has not been sufficiently studied. Setting the task, the purpose of the study. The purpose of the study is to analyze the theories of regional development in the context of the fourth industrial revolution and to propose an organizational and economic mechanism for the digital transformation of the regional business community, including the SMEs’ sector. Method or methodology for conducting research. The research used the methods of analogies, analysis and synthesis, sociological survey. Presentation of the main material (results of work). The article analyzes the main concepts of regional development, concludes that it is necessary to consolidate regional actors according to the ‘Quadruple Helix’ model based on inter-organizational information systems in order to introduce Industry 4.0 technologies. An algorithm for the development of an electronic platform from a cluster site to an information system of integrated supply chains is proposed on the example of the Novopolotsk innovative and industrial petrochemical cluster. The field of application of results. The results of the research can be used by companies providing activity in regional development and small business support, in scientific and educational institutions, in public administration. Conclusions according to the article. Networked connections between regional actors, innovation networks based on the open innovation paradigm and integrated supply chains promote region development in the context of the fourth industrial revolution, this requires appropriate institutional conditions.

Employment After Vocational Rehabilitation Predicts Decreased Health Care Utilization in Veterans With Mental Health Diagnoses.

Although the benefits of employment for veterans with mental health conditions are well-known, the effect of veterans' employment on a health system has not been evaluated. The purpose of this study was to evaluate the effect of veterans' employment (versus unemployment) on subsequent health care utilization in the Veterans Health Administration (VHA). This study used a sample of 29,022 veterans with mental health and substance use disorders who were discharged from VHA's employment services programs between fiscal years 2006 and 2010. Veterans' employment status (employed/unemployed) upon discharge from VHA employment programs was ascertained from program discharge forms and linked with VHA administrative health care utilization data for the subsequent 1- and 5-year periods. Multivariable ordinary least-squares and logistic regression models adjusted for site clustering and covariates indicated that employment (versus unemployment) predicted less health care utilization 1 year and 5 years post-discharge from employment services, including fewer outpatient mental health visits, homelessness services visits, employment services visits, primary care visits, and lower odds of mental health hospitalizations, mental health or vocational rehabilitation residential stays, and medical hospitalizations. Employment did not predict emergency department visits. VHA's investment in employment services for veterans with mental health and substance use disorders could reduce health care utilization system wide.

CSBD Healing in Rats after Application of Bovine Xenogeneic Biomaterial Enriched with Magnesium Alloy.

Xenogeneic biomaterials Cerbone® and OsteoBiol® are widely used in oral implantology. In dental practice, xenogeneic biomaterial is usually combined with autologous bone to provide bone volume stability needed for long-term dental implants. Magnesium alloy implants dissolve and form mineral corrosion layer that is directly in contact with bone tissue, allowing deposition of the newly formed bone. CSBD heals by intramembranous ossification and therefore is a convenient model for analyses of ostoconductive and osteoinductive properties of different type of biomaterials. Magnesium alloy-enriched biomaterials have not yet been applied in oral implantology. Therefore, the aim of the current study was to investigate biological properties of potentially new bovine xenogeneic biomaterial enriched with magnesium alloy in a 5 mm CSBD model. Osteoconductive properties of Cerabone®, Cerabone® + Al. bone, and OsteoBiol® were also analyzed. Dynamics of bone healing was followed up on the days 3, 7, 15, 21, and 30. Calvary bone samples were analyzed by micro-CT, and values of the bone morphometric parameters were assessed. Bone samples were further processed for histological and immunohistochemical analyses. Histological observation revealed CSBD closure at day 30 of the given xenogeneic biomaterial groups, with the exception of the control group. TNF-α showed high intensity of expression at the sites of MSC clusters that underwent ossification. Osx was expressed in pre-osteoblasts, which were differentiated into mature osteoblasts and osteocytes. Results of the micro-CT analyses showed linear increase in bone volume of all xenogeneic biomaterial groups and also in the control. The highest average values of bone volume were found for the Cerabone® + Mg group. In addition, less residual biomaterial was estimated in the Cerabone® + Mg group than in the Cerabone® group, indicating its better biodegradation during CSBD healing. Overall, the magnesium alloy xenogeneic biomaterial demonstrated key properties of osteoinduction and biodegradidibility during CSBD healing, which is the reason why it should be recommended for application in clinical practice of oral implantology.

Combinatorial CRISPR inversions of CTCF sites in HOXD cluster reveal complex insulator function

CTCF (CCCTC-binding factor) is a zinc-finger protein which plays a vital role in the three-dimensional (3D) genome architecture. A pair of forward-reverse convergent CTCF binding sites (CBS elements) mediates long-distance DNA interactions to form chromatin loops with the assistance of the cohesin complex, while CBS elements at the chromatin domain boundaries show reverse-forward divergent patterns and function as insulators to discriminate against DNA interaction between chromatin domains. However, there are still many unresolved problems regarding CTCF-mediated insulation function. In order to study the connections between chromatin loops and the insulation function of CBS elements, we combinatorically inverted CBS elements at the HOXD locus by using CRISPR/Cas9 DNA-fragment editing methods in the HEK293T cell line and obtained five different kinds of single-cell CRISPR clones. By performing quantitative high-resolution chromosome conformation capture copy (QHR-4C) experiments, we found that boundary CBS inversions abolish original chromatin loops and establish new loops from the opposite direction, thus shifting the insulator boundary to the new divergent CTCF sites. Furthermore, tandem CBS elements block cohesin permeated from the opposite orientation to function as insulators. RNA-seq experiments showed that alterations of local three-dimensional genome architecture would further influence gene expression of the HOXD cluster. In conclusion, a pair of divergent CBS elements function as insulators by forming chromatin loops within chromatin domains to block cohesin sliding.

Excitatory postsynaptic calcium transients at Aplysia sensory-motor neuron synapses allow for quantal examination of synaptic strength over multiple days in culture.

A more thorough description of the changes in synaptic strength underlying synaptic plasticity may be achieved with quantal resolution measurements at individual synaptic sites. Here, we demonstrate that by using a membrane targeted genetic calcium sensor, we can measure quantal synaptic events at the individual synaptic sites of Aplysia sensory neuron to motor neuron synaptic connections. These results show that synaptic strength is not evenly distributed between all contacts in these cultures, but dominated by multiquantal sites of synaptic contact, likely clusters of individual synaptic sites. Surprisingly, most synaptic contacts were not found opposite presynaptic varicosities, but instead at areas of pre- and postsynaptic contact with no visible thickening of membranes. The release probability, quantal size, and quantal content can be measured over days at individual synaptic contacts using this technique. Homosynaptic depression was accompanied by a reduction in release site probability, with no evidence of individual synaptic site silencing over the course of depression. This technique shows promise in being able to address outstanding questions in this system, including determining the synaptic changes that maintain long-term alterations in synaptic strength that underlie memory.

Electron Acceptor-Donor Iron Sites in the Iron-Sulfur Cluster of Photosynthetic Electron-Transfer Pathways.

In photosystem I, two electron-transfer pathways via quinones (A1A and A1B) are merged at the iron-sulfur Fe4S4 cluster FX into a single pathway toward the other two Fe4S4 clusters FA and FB. Using a quantum mechanical/molecular mechanical approach, we identify the redox-active Fe sites in the clusters. In FA and FB, the Fe site, which does not belong to the CxxCxxCxxxCP motif, serves as an electron acceptor/donor. FX has two independent electron acceptor Fe sites for A- and B-branch electron transfers, depending on the Asp-B575 protonation state, which causes the A1A-to-FX electron transfer to be uphill and the A1B-to-FX electron transfer to be downhill. The two asymmetric electron-transfer pathways from A1 to FX and the separation of the electron acceptor and donor Fe sites are likely associated with the specific role of FX in merging the two electron transfer pathways into the single pathway.