Showing papers by "Hungarian Academy of Sciences published in 2005"
TL;DR: After defining a set of new characteristic quantities for the statistics of communities, this work applies an efficient technique for exploring overlapping communities on a large scale and finds that overlaps are significant, and the distributions introduced reveal universal features of networks.
Abstract: A network is a network — be it between words (those associated with ‘bright’ in this case) or protein structures. Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of1,2,3,4. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins5,6, industrial sectors7 and groups of people8,9) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of communities, we apply an efficient technique for exploring overlapping communities on a large scale. We find that overlaps are significant, and the distributions we introduce reveal universal features of networks. Our studies of collaboration, word-association and protein interaction graphs show that the web of communities has non-trivial correlations and specific scaling properties.
5,217 citations
TL;DR: The IUPred server presents a novel algorithm for predicting such regions from amino acid sequences by estimating their total pairwise interresidue interaction energy, based on the assumption that IUP sequences do not fold due to their inability to form sufficient stabilizing inter Residue interactions.
Abstract: Summary: Intrinsically unstructured/disordered proteins and domains (IUPs) lack a well-defined three-dimensional structure under native conditions. The IUPred server presents a novel algorithm for predicting such regions from amino acid sequences by estimating their total pairwise interresidue interaction energy, based on the assumption that IUP sequences do not fold due to their inability to form sufficient stabilizing interresidue interactions. Optional to the prediction are built-in parameter sets optimized for predicting short or long disordered regions and structured domains.
Availability: The IUPred server is available for academic users at http://iupred.enzim.hu
Contact: [email protected]
1,954 citations
TL;DR: It is shown that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle, which explains why plants gain advantage from circadian control.
Abstract: Circadian clocks are believed to confer an advantage to plants, but the nature of that advantage has been unknown. We show that a substantial photosynthetic advantage is conferred by correct matching of the circadian clock period with that of the external light-dark cycle. In wild type and in long- and short-circadian period mutants of Arabidopsis thaliana, plants with a clock period matched to the environment contain more chlorophyll, fix more carbon, grow faster, and survive better than plants with circadian periods differing from their environment. This explains why plants gain advantage from circadian control.
1,276 citations
TL;DR: The potential of Piriformospora indica to induce resistance to fungal diseases and tolerance to salt stress in the monocotyledonous plant barley is reported on.
Abstract: Disease resistance strategies are powerful approaches to sustainable agriculture because they reduce chemical input into the environment. Recently, Piriformospora indica, a plant-root-colonizing basidiomycete fungus, has been discovered in the Indian Thar desert and was shown to provide strong growth-promoting activity during its symbiosis with a broad spectrum of plants [Verma, S. et al. (1998) Mycologia 90, 896-903]. Here, we report on the potential of P. indica to induce resistance to fungal diseases and tolerance to salt stress in the monocotyledonous plant barley. The beneficial effect on the defense status is detected in distal leaves, demonstrating a systemic induction of resistance by a root-endophytic fungus. The systemically altered “defense readiness” is associated with an elevated antioxidative capacity due to an activation of the glutathione-ascorbate cycle and results in an overall increase in grain yield. Because P. indica can be easily propagated in the absence of a host plant, we conclude that the fungus could be exploited to increase disease resistance and yield in crop plants.
1,197 citations
TL;DR: It is proposed that the hierarchical organization of ambient oscillatory activity allows auditory cortex to structure its temporal activity pattern so as to optimize the processing of rhythmic inputs.
Abstract: EEG oscillations are hypothesized to reflect cyclical variations in the neuronal excitability, with particular frequency bands reflecting differing spatial scales of brain operation. However, despite decades of clinical and scientific investigation, there is no unifying theory of EEG organization, and the role of ongoing activity in sensory processing remains controversial. This study analyzed laminar profiles of synaptic activity [current source density CSD] and multiunit activity (MUA), both spontaneous and stimulus-driven, in primary auditory cortex of awake macaque monkeys. Our results reveal that the EEG is hierarchically organized; delta (1-4 Hz) phase modulates theta (4-10 Hz) amplitude, and theta phase modulates gamma (30-50 Hz) amplitude. This oscillatory hierarchy controls baseline excitability and thus stimulus-related responses in a neuronal ensemble. We propose that the hierarchical organization of ambient oscillatory activity allows auditory cortex to structure its temporal activity pattern so as to optimize the processing of rhythmic inputs.
1,166 citations
Aarhus University1, University of Florida2, University of Savoy3, St. Johns River Water Management District4, Brandenburg University of Technology5, University of Washington6, University of Tartu7, University of Liverpool8, Swedish University of Agricultural Sciences9, Environment Agency10, University of Konstanz11, Hungarian Academy of Sciences12
TL;DR: In this article, the authors examined 35 long-term (5-35 years, mean: 16 years) lake re-oligotrophication studies and found that external total phosphorus loading resulted in lower in-lake TP concentration, lower chlorophyll a (chl a) concentration and higher Secchi depth in most lakes.
Abstract: SUMMARY 1. This synthesis examines 35 long-term (5–35 years, mean: 16 years) lake re-oligotrophication studies. It covers lakes ranging from shallow (mean depth <5 m and/or polymictic) to deep (mean depth up to 177 m), oligotrophic to hypertrophic (summer mean total phosphorus concentration from 7.5 to 3500 l gL )1 before loading reduction), subtropical to temperate (latitude: 28–65� ), and lowland to upland (altitude: 0–481 m). Shallow northtemperate lakes were most abundant. 2. Reduction of external total phosphorus (TP) loading resulted in lower in-lake TP concentration, lower chlorophyll a (chl a) concentration and higher Secchi depth in most lakes. Internal loading delayed the recovery, but in most lakes a new equilibrium for TP
1,126 citations
TL;DR: IUPred, a novel method for estimating the total pairwise interaction energy of proteins of known structure, based on a quadratic form in the amino acid composition of the protein, is presented and substantiates the concept of protein disorder.
966 citations
TL;DR: In this article, a real data set is used to show that there are often zeros in abundance distributions which maximize functional diversity and that Rao's quadratic entropy (FDQ) is a suitable measure of functional diversity if several traits are considered.
Abstract: Question: Is Rao's quadratic entropy a suitable measure of functional diversity if several traits are considered? Methods: It is checked whether Rao's quadratic entropy (FDQ) satisfies a priori criteria suggested by Mason et al. A real data set is used to show that there are often zeros in abundance distributions which maximize functional diversity. Results and Conclusion: FDQ fulfils all a priori criteria and it surpasses other proposed indices, because it includes species abundances and more than one trait. Therefore, it seems to be an improvement compared to measures of functional diversity that are currently available. An unexpected property of FDQ is that its value may decrease if species richness increases. The reason is that functional diversity is influenced by both species-abundance based diversity and differences among species. Introduction of a new species into the community increases the species-abundance based diversity, while it may decrease the average dissimilarity among species. ...
893 citations
TL;DR: Cinchona alkaloid-derived chiral bifunctional thiourea organocatalysts were synthesized and applied in the Michael addition between nitromethane and chalcones with high ee and chemical yields.
862 citations
TL;DR: Novel advances in the rapidly advancing field of IUPs are reviewed, with the major attention directed to the evidence of their unfolded character in vivo, the interplay of their residual structure and their various functional modes and the functional benefits their malleable structural state provides.
701 citations
TL;DR: Though recent advances resulted in development of improved in vitro BBB model systems to investigate disease modeling, drug screening, and testing vectors targeting the brain, there is a need for checking validity of permeability models and cautious interpretation of data.
Abstract: 1. The specifically regulated restrictive permeability barrier to cells and molecules is the most important feature of the blood–brain barrier (BBB). The aim of this review was to summarize permeability data obtained on in vitro BBB models by measurement of transendothelial electrical resistance and by calculation of permeability coefficients for paracellular or transendothelial tracers.
TL;DR: In this article, the VRN-1 gene was sequenced and all the accessions had large deletions within the first intron, which overlap in a 4-kb region and showed high sequence conservation among the different recessive alleles.
Abstract: The broad adaptability of wheat and barley is in part attributable to their flexible growth habit, in that spring forms have recurrently evolved from the ancestral winter growth habit. In diploid wheat and barley growth habit is determined by allelic variation at the VRN-1 and/or VRN-2 loci, whereas in the polyploid wheat species it is determined primarily by allelic variation at VRN-1. Dominant Vrn-A1 alleles for spring growth habit are frequently associated with mutations in the promoter region in diploid wheat and in the A genome of common wheat. However, several dominant Vrn-A1, Vrn-B1, Vrn-D1 (common wheat) and Vrn-H1 (barley) alleles show no polymorphisms in the promoter region relative to their respective recessive alleles. In this study, we sequenced the complete VRN-1 gene from these accessions and found that all of them have large deletions within the first intron, which overlap in a 4-kb region. Furthermore, a 2.8-kb segment within the 4-kb region showed high sequence conservation among the different recessive alleles. PCR markers for these deletions showed that similar deletions were present in all the accessions with known Vrn-B1 and Vrn-D1 alleles, and in 51 hexaploid spring wheat accessions previously shown to have no polymorphisms in the VRN-A1 promoter region. Twenty-four tetraploid wheat accessions had a similar deletion in VRN-A1 intron 1. We hypothesize that the 2.8-kb conserved region includes regulatory elements important for the vernalization requirement. Epistatic interactions between VRN-H2 and the VRN-H1 allele with the intron 1 deletion suggest that the deleted region may include a recognition site for the flowering repression mediated by the product of the VRN-H2 gene of barley.
TL;DR: In this article, the optical properties of humic-like substances (HULIS) isolated from the fine fraction of biomass-burning aerosol collected in the Amazon basin during the LBA-SMOCC (Large scale Biosphere atmosphere experiment in Amazonia? SMOke aerosols, Clouds, rainfall and Climate) experiment in September 2002 were analyzed.
Abstract: We present here the optical properties of humic-like substances (HULIS) isolated from the fine fraction of biomass-burning aerosol collected in the Amazon basin during the LBA-SMOCC (Large scale Biosphere atmosphere experiment in Amazonia ? SMOke aerosols, Clouds, rainfall and Climate) experiment in September 2002. From the isolated HULIS, aerosol particles were generated and their scattering and absorption coefficients measured. The size distribution and mass of the particles were also recorded. The value of the index of refraction was derived from "closure" calculations based on particle size, scattering and absorption measurements. On average, the complex index of refraction at 532 nm of HULIS collected during day and nighttime was 1.65?0.0019i and 1.69?0.0016i, respectively. In addition, the imaginary part of the complex index of refraction was calculated using the measured absorption coefficient of the bulk HULIS. The mass absorption coefficient of the HULIS at 532 nm was found to be quite low (0.031 and 0.029 m2 g?1 for the day and night samples, respectively). However, due to the high absorption Angstrom exponent (6?7) of HULIS, the specific absorption increases substantially towards shorter wavelengths (~2?3 m2 g?1 at 300 nm), causing a relatively high (up to 50%) contribution to the light absorption of our Amazonian aerosol at 300 nm. For the relative contribution of HULIS to light absorption in the entire solar spectrum, lower values (6.4?8.6%) are obtained, but those are still not negligible.
TL;DR: A major emphasis of this review will be on target site location and the mechanism of catalysis, two problems currently being addressed in the literature.
Abstract: Type II restriction endonucleases are components of restriction modification systems that protect bacteria and archaea against invading foreign DNA. Most are homodimeric or tetrameric enzymes that cleave DNA at defined sites of 4-8 bp in length and require Mg2+ ions for catalysis. They differ in the details of the recognition process and the mode of cleavage, indicators that these enzymes are more diverse than originally thought. Still, most of them have a similar structural core and seem to share a common mechanism of DNA cleavage, suggesting that they evolved from a common ancestor. Only a few restriction endonucleases discovered thus far do not belong to the PD...D/ExK family of enzymes, but rather have active sites typical of other endonuclease families. The present review deals with new developments in the field of Type II restriction endonucleases. One of the more interesting aspects is the increasing awareness of the diversity of Type II restriction enzymes. Nevertheless, structural studies summarized herein deal with the more common subtypes. A major emphasis of this review will be on target site location and the mechanism of catalysis, two problems currently being addressed in the literature.
TL;DR: It is suggested that intrinsically unstructured proteins (IUPs) might provide radically different mechanisms that give rise to unprecedented cases of moonlighting by eliciting opposing (inhibiting and activating) action on different partners or even the same partner molecule.
TL;DR: It is proposed that alpha-KGDH is a key factor in a vicious cycle by which oxidative stress is induced and promoted in nerve terminals, and could substantially contribute to generation of oxidative stress due to inhibition of complex I.
Abstract: Overwhelming evidence has accumulated indicating that oxidative stress is a crucial factor in the pathogenesis of neurodegenerative diseases. The major site of production of superoxide, the primary reactive oxygen species (ROS), is considered to be the respiratory chain in the mitochondria, but the exact mechanism and the precise location of the physiologically relevant ROS generation within the respiratory chain have not been disclosed as yet. Studies performed with isolated mitochondria have located ROS generation on complex I and complex III, respectively, depending on the substrates or inhibitors used to fuel or inhibit respiration. A more "physiological" approach is to address ROS generation of in situ mitochondria, which are present in their normal cytosolic environment. Hydrogen peroxide formation in mitochondria in situ in isolated nerve terminals is enhanced when complex I, complex III, or complex IV is inhibited. However, to induce a significant increase in ROS production, complex III and comple...
TL;DR: Several new families have been discovered, in which the nucleophile-base-acid pattern is generally conserved, but the individual components can vary, illustrating how different groups and different protein structures achieve the same reaction.
Abstract: The catalytic action of serine peptidases depends on the interplay of a nucleophile, a general base and an acid. In the classic trypsin and subtilisin families this catalytic triad is composed of serine, histidine and aspartic acid residues and exhibits similar spatial arrangements, but the order of the residues in the amino acid sequence is different. By now several new families have been discovered, in which the nucleophile-base-acid pattern is generally conserved, but the individual components can vary. The variations illustrate how different groups and different protein structures achieve the same reaction.
TL;DR: The pathological relevance of these two features of α-KGDH is discussed in this review, particularly in relation to neurodegeneration, as an impaired function of this enzyme has been found to be characteristic for several Neurodegenerative diseases.
Abstract: Alpha-ketoglutarate dehydrogenase (α-KGDH) is a highly regulated enzyme, which could determine the metabolic flux through the Krebs cycle. It catalyses the conversion of α-ketoglutarate to succinyl-CoA and produces NADH directly providing electrons for the respiratory chain. α-KGDH is sensitive to reactive oxygen species (ROS) and inhibition of this enzyme could be critical in the metabolic deficiency induced by oxidative stress. Aconitase in the Krebs cycle is more vulnerable than α-KGDH to ROS but as long as α-KGDH is functional NADH generation in the Krebs cycle is maintained. NADH supply to the respiratory chain is limited only when α-KGDH is also inhibited by ROS. In addition being a key target, α-KGDH is able to generate ROS during its catalytic function, which is regulated by the NADH/NAD+ ratio. The pathological relevance of these two features of α-KGDH is discussed in this review, particularly in relation to neurodegeneration, as an impaired function of this enzyme has been found to be characteristic for several neurodegenerative diseases.
TL;DR: It is shown that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chlorop last.
Abstract: In contrast to animal and fungal cells, green plant cells contain one or multiple chloroplasts, the organelle(s) in which photosynthetic reactions take place. Chloroplasts are believed to have originated from an endosymbiotic event and contain DNA that codes for some of their proteins. Most chloroplast proteins are encoded by the nuclear genome and imported with the help of sorting signals that are intrinsic parts of the polypeptides. Here, we show that a chloroplast-located protein in higher plants takes an alternative route through the secretory pathway, and becomes N-glycosylated before entering the chloroplast.
TL;DR: The role of IKs in normal human ventricular muscle and in preparations in which both repolarization reserve was attenuated and sympathetic activation was increased by exogenous dofetilide and adrenaline is elucidated, playing an increasingly important role in limiting action potential prolongation.
Abstract: Background— Although pharmacological block of the slow, delayed rectifier potassium current (IKs) by chromanol 293B, L-735,821, or HMR-1556 produces little effect on action potential duration (APD) in isolated rabbit and dog ventricular myocytes, the effect of IKs block on normal human ventricular muscle APD is not known. Therefore, studies were conducted to elucidate the role of IKs in normal human ventricular muscle and in preparations in which both repolarization reserve was attenuated and sympathetic activation was increased by exogenous dofetilide and adrenaline. Methods and Results— Preparations were obtained from undiseased organ donors. Action potentials were measured in ventricular trabeculae and papillary muscles using conventional microelectrode techniques; membrane currents were measured in ventricular myocytes using voltage-clamp techniques. Chromanol 293B (10 μmol/L), L-735,821 (100 nmol/L), and HMR-1556 (100 nmol/L and 1 μmol/L) produced a <12-ms change in APD while pacing at cycle lengths ...
TL;DR: AMPA receptor-mediated recurrent excitation was necessary for the synchronization of interneuronal discharge, which strongly supports a synaptic feedback model for the generation of hippocampal gamma oscillations.
TL;DR: Basic knowledge of ETEC infections in veterinary medicine is summarized and attention is paid to recently described new virulence factors and to new genetic vectors in ETEC bacteria.
TL;DR: The findings suggest that P. acnes modulates the antimicrobial peptide and chemokine expression of keratinocytes and thereby contributes to the recruitment of inflammatory cells to the sites of infections.
Southwest Research Institute1, California Institute of Technology2, University College London3, Rutherford Appleton Laboratory4, Rice University5, University of Virginia6, University of Oulu7, Goddard Space Flight Center8, Hungarian Academy of Sciences9, Los Alamos National Laboratory10, University of Montana11
TL;DR: Over the A and B rings, an ionosphere in which O2+ and O+ are dominant is found, which suggests the possible existence of a layer of O2 gas similar to the atmospheres of Europa and Ganymede.
Abstract: During Cassini9s initial orbit, we observed a dynamic magnetosphere composed primarily of a complex mixture of water-derived atomic and molecular ions. We have identified four distinct regions characterized by differences in both bulk plasma properties and ion composition. Protons are the dominant species outside about 9 R S (where R S is the radial distance from the center of Saturn), whereas inside, the plasma consists primarily of a corotating comet-like mix of water-derived ions with ∼3% N + . Over the A and B rings, we found an ionosphere in which O 2 + and O + are dominant, which suggests the possible existence of a layer of O 2 gas similar to the atmospheres of Europa and Ganymede.
TL;DR: This work combined multiple immunolabeling with whole-cell recordings to investigate the morpho-functional characteristics of cannabinoid signaling in rat somatosensory cortex and found a unique population of large pyramidal neurons in layer VB that received much less perisomatic innervation from CB1-expressing GABAergic axon terminals and, accordingly, showed no depolarization-induced suppression of inhibition.
Abstract: Endocannabinoid-mediated retrograde signaling exerts powerful control over synaptic transmission in many brain areas. However, in the neocortex, the precise laminar, cellular, and subcellular localization of the type 1 cannabinoid receptor (CB1) as well as its function has been elusive. Here we combined multiple immunolabeling with whole-cell recordings to investigate the morpho-functional characteristics of cannabinoid signaling in rat somatosensory cortex. Immunostaining for CB1 revealed axonal and somatic labeling with striking layer specificity: a high density of CB1-positive fibers was seen in layers II-III, in layer VI, and in upper layer V, whereas other layers had sparse (layer IV) or hardly any (layer I) staining. Membrane staining for CB1 was only found in axon terminals, all of which contained GABA and formed symmetric synapses. Double immunostaining also revealed that CB1-positive cells formed two neurochemically distinct subpopulations: two-thirds were cholecystokinin positive and one-third expressed calbindin, each subserving specific inhibitory functions in cortical networks. In addition, cannabinoid sensitivity of GABAergic input showed striking layer specificity, as revealed by both electrophysiological and anatomical experiments. We found a unique population of large pyramidal neurons in layer VB that received much less perisomatic innervation from CB1-expressing GABAergic axon terminals and, accordingly, showed no depolarization-induced suppression of inhibition, unlike pyramidal cells in layer II, and a population of small pyramidal cells in layer V. This suggests that inhibitory control of pyramidal cells involved in intracortical or corticostriatal processing is fine-tuned by activity-dependent endocannabinoid signaling, whereas inhibition of pyramidal cells relaying cortical information to lower subcortical effector centers often lacks this plasticity.
TL;DR: A novel algorithm is achieved by a novel algorithm that precomputes a compact database; using this database, it can serve online responses to arbitrary user-selected personalization and proves that for a fixed error probability the size of the database is linear in the number of web pages.
Abstract: Personalized PageRank expresses link-based page quality around userselected pages in a similar way as PageRank expresses quality over the entire web. Existing personalized PageRank algorithms can, however, serve online queries only for a restricted choice of pages. In this paper we achieve full personalization by a novel algorithm that precomputes a compact database; using this database, it can serve online responses to arbitrary user-selected personalization. The algorithm uses simulated random walks; we prove that for a fixed error probability the size of our database is linear in the number of web pages. We justify our estimation approach by asymptotic worst-case lower bounds: we show that on some sets of graphs, exact personalized PageRank values can only be obtained from a database of size quadratic in the number of vertices. Furthermore, we evaluate the precision of approximation experimentally on the Stanford WebBase graph.
TL;DR: The results suggest that the absorbing film-assisted laser-induced forward transfer technique appears to be suitable for several potential applications in tissue engineering and the biomedical tissue repair technologies.
Abstract: The survival, proliferation, and differentiation of freshly isolated and cultured cells were studied after absorbing film-assisted laser-induced forward transfer. Rat Schwann and astroglial cells and pig lens epithelial cells were used for transfer and the cells were cultured for 2 weeks after laser-pulsed transfer. All three cell types survived, proliferated, and differentiated under cell culture conditions and regained their original phenotype a few days after cell transfer. Time resolution studies have shown that the time required to accelerate the jets and droplets containing the cells was less than 1 micros and that the estimated minimum average acceleration of those ejected cells that reached a constant velocity was approximately 10(7) x g. This suggests that the majority of studied cells tolerated the extremely high acceleration at the beginning of the ejection and the deceleration during impact on the acceptor plate without significant damage to the original phenotype. These results suggest that the absorbing film-assisted laser-induced forward transfer technique appears to be suitable for several potential applications in tissue engineering and the biomedical tissue repair technologies.
Argonne National Laboratory1, University of Texas at Austin2, Technion – Israel Institute of Technology3, Eötvös Loránd University4, University of Graz5, Weizmann Institute of Science6, École Polytechnique Fédérale de Lausanne7, University of Massachusetts Amherst8, University of Stuttgart9, Hungarian Academy of Sciences10
TL;DR: In this paper, the first part of a series of articles reporting critically evaluated thermochemical properties of selected free radicals is presented, including the enthalpy of formation, as well as the heat capacity, integrated heat capacity and entropy of the radicals.
Abstract: This is the first part of a series of articles reporting critically evaluated thermochemical properties of selected free radicals. The present article contains datasheets for 11 radicals: CH, CH2(triplet), CH2(singlet), CH3, CH2OH, CH3O, CH3CO, C2H5O, C6H5CH2, OH, and NH2. The thermochemical properties discussed are the enthalpy of formation, as well as the heat capacity, integrated heat capacity, and entropy of the radicals. One distinguishing feature of the present evaluation is the systematic utilization of available kinetic, spectroscopic and ion thermochemical data as well as high-level theoretical results.
TL;DR: The use of multiphase, multicomponent materials is expected to grow with a larger than average rate also in the future as mentioned in this paper, and it is important to keep the interdisciplinary nature of the area since principles and techniques developed by one field may find application also in other areas.
TL;DR: The presence/absence of the tightly linked ZCCT-H gene family members on chromosome 4H perfectly correlates with growth habit and it is concluded that one of the three ZCCt-H genes is VRN-H2.
Abstract: Vernalization, the requirement of a period of low temperature to induce transition from the vegetative to reproductive state, is an evolutionarily and economically important trait in the Triticeae. The genetic basis of vernalization in cultivated barley (Hordeum vulgare subsp. vulgare) can be defined using the two-locus VRN-H1/VRN-H2 model. We analyzed the allelic characteristics of HvBM5A, the candidate gene for VRN-H1, from ten cultivated barley accessions and one wild progenitor accession (subsp. spontaneum), representing the three barley growth habits – winter, facultative, and spring. We present multiple lines of evidence, including sequence, linkage map location, and expression, that support HvBM5A being VRN-H1. While the predicted polypeptides from different growth habits are identical, spring accessions contain a deletion in the first intron of HvBM5A that may be important for regulation. While spring HvBM5A alleles are typified by the intron-localized deletion, in some cases, the promoter may also determine the allele type. The presence/absence of the tightly linked ZCCT-H gene family members on chromosome 4H perfectly correlates with growth habit and we conclude that one of the three ZCCT-H genes is VRN-H2. The VRN-H2 locus is present in winter genotypes and deleted from the facultative and spring genotypes analyzed in this study, suggesting the facultative growth habit (cold tolerant, vernalization unresponsive) is a result of deletion of the VRN-H2 locus and presence of a winter HvBM5A allele. All reported barley vernalization QTLs can be explained by the two-locus VRN-H1/VRN-H2 model based on the presence/absence of VRN-H2 and a winter vs. spring HvBM5A allele.