Definite Sequence Research Articles

Primary, secondary, and admixture zonation of copper-nickel ores during fractional crystallization of sulfide melts

Results of the study of massive ore bodies of mag� matic copper–nickel deposits demonstrate their het� erogeneous structure by mineral assemblages in vari� ous parts of the ore body, as well as by average chemical composition. Moreover, these characteristics may change spasmodically within the ore body. Conse� quently a definite sequence of zones with various ore types is formed in it [1–3]. Such sequences are not necessarily the same in different deposits, but accu� mulated results provide evidence for some similarity of the deposit structure and allow us to classify them by zonation types. The relation between such types and the average chemical composition of ores is evident. A number of reviews on description and primary classi� fication of varieties of ore body zonation for individual groups of deposits are available in the literature [1–5]. Explanation of this phenomenon involves concepts on the sequence of the phase formation during crystalli� zation of multicomponent melts of the Cu–Fe–Ni–S system. Data on mineralogical heterogeneity of ore bodies, as well as chemical heterogeneity of individual zones (chemical zonation), are available in the literature [6, 7]. It is controlled by both regularities of initial crystallization of sulfide melt and peculiarities of sub� solidus decomposition of initial phases. To understand the reasons for the zoned structure of ore bodies, we have to know the physicochemical history of their for� mation (namely, the time dependence of distribution of temperature and concentrations of components within the volume of the ore body during its cooling). Physicochemical reconstruction of the genetic history of the deposits is based on knowledge of phase rela�

A Proteomic-Based Approach for Detection of Chicken in Meat Mixes

A proteomic-based method has been developed for the detection of chicken meat within mixed meat preparations. The procedure is robust and simple, comprising the extraction of myofibrillar proteins, enrichment of target proteins using OFFGEL isoelectric focusing, in-solution trypsin digestion of myosin light chain 3, and analysis of the generated peptides by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Using this approach, it was possible for example to detect 0.5% contaminating chicken in pork meat with high confidence. Quantitative detection of chicken meat was done by using AQUA stable isotope peptides made from the sequence of previously selected species-specific peptide biomarkers. Linearity was observed between the amount of the peptide biomarker and the amount of chicken present in the mixture; further independent replication is required now to validate the method. Apart from its simplicity, this approach has the advantage that it can be used effectively for the detection of both raw and cooked meat. The method is robust, reliable, and sensitive, representing a serious alternative to methods currently in use for these purposes. It is amenable to highly processed foods which can be particularly problematic, as the tertiary protein structure is often affected in processed food precluding immunoassays. In addition, this proteomic analysis will permit the determination of definitive discriminatory sequence, unlike the DNA PCR based methods used presently. The present article also demonstrates the translation of the technology to routine mass spectrometry equipment, making the methodology suitable for public analysts.

Unique structural characteristics and evolution of a cluster of venom phospholipase A 2 isozyme genes of Protobothrops flavoviridis snake

Protobothrops flavoviridis (Crotalinae) venom gland phospholipase A 2 (PLA 2) isozyme genes have evolved in an accelerated manner to acquire diverse physiological activities in their products. For elucidation of the multiplication mechanism of PLA 2 genes, a 25,026 bp genome segment harboring five PLA 2 isozyme genes was obtained from Amami-Oshima P. flavoviridis liver and sequenced. The gene PfPLA 2 encoded [Lys 49]PLA 2 called BPII, the gene PfPLA 4 neurotoxic [Asp 49]PLA 2 called PLA-N, the gene PfPLA 5 basic [Asp 49]PLA 2 called PLA-B, and PfPLA 1(ψ) and PfPLA 3(ψ) were the inactivated genes. The 5′ truncated reverse transcriptase (RT) elements, whose intact forms constitute long interspersed nuclear elements (LINEs), were found in close proximity to the 3′ end of PLA 2 genes and named PLA 2 gene-coupled RT fragments (PcRTFs). The facts that PcRTFs have the stem–loop and repetitive sequence in the 3′ untranslated region (UTR) which is characteristic of CR1 LINEs suggest that PcRTFs are the debris of P. flavoviridis ancestral CR1 LINEs, denoted as PfCR1s. Since the associated pairs of PLA 2 genes and PcRTFs are arranged in tandem in the 25,026 bp segment, it is thought that an ancestral PLA 2 gene- PfCR1 unit ( PfPLA- PfCR1) which was produced by retrotransposition of PfCR1 by itself to the 3′ end of PLA 2 gene duplicated several times to form a multimer of PfPLA- PfCR1, a cluster of PLA 2 genes, in the period after Crotalinae and Viperinae snakes branched off. Recombinational hot spot of a 37 bp segment, named Scomb, was found in the region 548 bp upstream from the TATA box of PLA 2 genes. Thus, it could be assumed that multiplication of PfPLA- PfCR1 occurred by unequal crossing over of the segment, - Scomb- PfPLA- PfCR1- Scomb-. The PfCR1 moieties were afterward disrupted in the 5′ portion to PcRTFs. The detection of two types of PcRTFs different in length which were produced by elimination of two definitive sequences in PfCR1 moiety possibly by gene conversion clearly supports such process but not multiplication of the PLA 2 gene-PcRTF unit.

Efficacy of N-methanocarbathymidine Against Herpes Simplex Virus is Cell Cycle Dependent

Exanthematic and papulo-vesicular lesions in the udder and teats of milking cows are fairly common in some Brazilian dairies, especially those with poor sanitary conditions and hand milking. The orthopoxvirus Vaccinia virus (VACV) and the parapoxviruses Pseudocowpox virus (PCPV) and Bovine popular stomatitis virus (BPSV) have been frequently associated with such conditions. Elsewhere, Bovine herpesvirus 2 (BoHV-2) has also been associated with similar clinical signs. Thus, we herein describe a conventional multiplex PCR designed to detect the genome of these viruses in clinical samples while differentiating among them by amplicon size. For this, primer sets targeting the orthopoxvirus vascular growth factor (amplicon size 292 bp), PCPV (374 bp) and BSPV (607 bp) B2L genes, and the BoHV-2 DNA polymerase gene (138 bp) were selected. The chosen primers anneal within the same temperature range and do not interfere with each other during the PCR amplification. PCR conditions were initially standardized for each agent in individual PCR reactions firstly using the target virus as positive control followed by using a mixture of all four virues. Lastly, a multiplex PCR containing the four sets of primers was set up to amplify all four targeted viruses in one reaction. The multiplex PCR was able to detect DNA extracted from cell culture supernatants containing 20 TCID50 of BoHV-2 and 50 TCID50 of VACV. Further, the test could detect the viral genomes in 1:10, 1:50 and 1:1000 dilutions of total DNA extracted from clinical specimens (e.g. scabs, crusts) of natural cases (PCPV, VACV and BPSV) and 1:10 dilutions of DNA extracted from scabs collected from BoHV-2 experimentally infected cattle. A possible amplification of other orthopoxviruses, predicted by in silico analysis, was considered to not represent an important pitfall since these are exotic in Brazil, very rare, or viruses not associated with cattle. For definitive agent identification amplicon sequencing needs to be conducted. Thus, this multiplex PCR seems suitable for initial detection and identification of the agents involved in exanthematic and vesicular disease, providing a sensitive and specific diagnosis for such conditions in dairy cows.

„Stargana za trzewia publiczność opadła jak jeden flak”. Witkacego spektakle potencjalne

Witkacy’s well-known Pure Form in Theatre Theory constitutes, from the logical point of view, a sequence of paradoxical definitions and surrealistic examples. It is, undoubtedly, a premeditated tactics of the Author. Witkacy deliberately aspired to make a mess in the reader's (or, in fact, implied spectator’s) brain, and discreetly intervowen in principal specimen’s content own anthropological experience, collected in an Australian expedition. Finally, in the visionary novel Insatiability, Witkacy smashed up his concept of metaphysical theatre, impossible in the future stupefied society.

A proposito di hyp . II LGRQA Soph. Ph . Dain: Aristofane di bisanzio e la cosiddetta rubrica della MYΘOΓOΠA

A small number of scholarly hypotheseis to the Greek tragedies are expressly attributed in several medieval manuscripts to Aristophanes of Byzantium, while other hypotheseis with the same subjects and formal characteristics do not name the author. The actual role that could be awarded to the great Alexandrian philologist is heavily debated until today. No single hypothesis of the Aristophanes’ type is preserved in its original condition: only in the fewest cases have the copyists adopted the constitutive rubrics almost entirely; the major part was more often left out. Nevertheless, a definite sequence has been observed in the order of the preserved rubrics, most of which are characterized by repeated linguistic formulae . The rubrics that can be identified contain these elements: a very brief synopsis, μνϑgoπgoiiα, locus actionis — compositio chori — persona prologi , τό κɛφάλαigoν, didascalia , an aesthetic judgement, τά τgoiδράματgoς πρόσωπα.The following article does not question the genuine character ...

The Combination of Romidepsin and Bortezomib Results in Synergistic Induction of Apoptosis in Human B-Lymphoma Cell Lines.

Abstract 1689Poster Board I-715 IntroductionThe use of the proteasome inhibitor bortezomib has demonstrated activity in multiple myeloma and lymphomas. The HDAC inhibitor romidepsin is being evaluated in CTCL and PTCL, though its activity in B-cell lymphomas is less clear. We hypothesized that the combination of bortezomib and romidepsin would result in synergistic apoptosis in different B-cell NHL cell lines based upon the observed activity of this combination in more mature B-cell malignancies such as myeloma. Experimental DesignDaudi, HT, Ramos and SUDHL-4 cell lines were exposed to different concentrations of bortezomib and romidepsin, separately, concurrently, and sequentially. Cell viability was assessed using MTT-assay, induced apoptosis was evaluated using Annexin V and PI staining from 24-48 hours. Apoptosis was also evaluated using western blot analysis of caspases and PARP cleavage. LC3 and HDAC6 level expressions were performed to determine if the effect of the combination was a result of the aggresome or autophagy pathway. Cell cycle studies were also performed to study if there were any changes after treating cells with the combination. ResultsThe combination of bortezomib and romidepsin resulted in synergistic B-cell apoptosis as measured by MTT-assay with combination indices of < 0.5. This was associated with increased caspases and PARP cleavage as early as 24 hours after exposure. Order of addition experiments demonstrated definite sequence specificity. When romidepsin was added first, and 6 hours later followed by bortezomib, apoptosis was enhanced, compared to both agents being given concurrently or when bortezomib was administered first. Cell cycle analysis studies demonstrated that pretreatment of cells with romidepsin for 6 hours followed by the addition of bortezomib arrested the cells in G2M phase. HDAC6 expression was significantly reduced following combination therapy, and LC3-I was cleaved to LC3-II in treated cells suggesting that the combination affected aggresome formation and autophagy. ConclusionThe combination of romidepsin and bortezomib at low nanomolar concentrations suggests that this may be an important clinical combination to test in patients with relapsed or refractory B-cell malignancies. Sequence of administration data is currently being tested to determine if the effect is a result of autophagy inhibition as is seen in myeloma cell lines. Additional mechanistic studies will be presented with the goals of identifying predictors of response that can then be validated in prospective clinical trials. DisclosuresLechowicz:Gloucester: Consultancy. Kaufman:Millennium: Consultancy; Genzyme: Consultancy; Celgene: Consultancy; Merck: Research Funding; Celgene: Research Funding. Lonial:Gloucester: Research Funding; Novartis: Consultancy; BMS: Consultancy; Millennium: Consultancy, Research Funding; Celgene: Consultancy. Flowers:Millennium: Research Funding.

A special class of polynomials related to non-classic general interpolatory problems

The class of polynomials L k (x), k=1, 2, …, of degree 2k+1 satisfying the differential equation L″ k (x)=L k−1(x) and the initial condition L k (0)=0 is introduced. For any choice of one more condition, we have a definite and special sequence of polynomials. The sequences of polynomials related to a linear functional F on C 2k+1 are interesting, since they are the basis of a particular non-classic interpolatory problem.

Complexity Reduction Techniques for the Compression of High-Definition Video

The state-of-the-art video compression standard, the hybrid predictive-transform H.264/AVC codec, has lead to substantial performance improvement compared to other existing standards. Performing predictions is a computational demanding task and optimizing this stage may result in substantial encoding speedup. In this paper, we propose more efficient approaches to implement the H.264/AVC prediction stage. The first idea is to use original data rather than reconstructed ones to perform prediction tests before choosing the best mode. The residue, however, is evaluated using previously decoded data in order to avoid drifting. The second approach is to employ a subset of dominant prediction modes instead of testing all modes recommended by the H.264/AVC standard. The subset is updated frame-by-frame using macroblock sampling. Results for high definition sequences show that the quality loss is negligible allowing us not only to parallelize the inter-prediction stage but also to reduce total complexity.

Star Formation from Spitzer (Lyman) to Spitzer (Space Telescope) and Beyond11Conference was held in Vienna on 2008 September 10–12, and was part of the European Astronomical Society’s JENAM 2008.

Star Formation from Spitzer (Lyman) to Spitzer (Space Telescope) and Beyond11Conference was held in Vienna on 2008 September 10–12, and was part of the European Astronomical Society’s JENAM 2008.

Sequence determinants of innate immune activation by short interfering RNAs

BackgroundShort interfering RNAs (siRNAs) have been shown to induce immune stimulation through a number of different receptors in a range of cell types. In primary cells, both TLR7 and TLR8 have been shown to recognise siRNAs however, despite the identification of a number of TLR7/8 stimulatory RNA motifs, the complete and definitive sequence determinants of TLR7 and TLR8 are yet to be elucidated.ResultsA total of 207 siRNA sequences were screened for TLR7/8 stimulation in human PBMCs. There was a significant correlation between the U count of the U-rich strand and the immunostimulatory activity of the duplex. Using siRNAs specifically designed to analyse the effect of base substitutions and hybridisation of the two strands, we found that sequence motifs and the thermodynamic properties of the duplexes appeared to be the major determinants of siRNA immunogenicity and that the strength of the hybridisation interaction between the two strands correlated negatively with immunostimulatory activity.ConclusionThe data presented favour a model of TLR7/8 activation by siRNAs, in which the two strands are denatured in the endosome, and single-stranded, U-rich RNA species activate TLR7/8. These findings have relevance to the design of siRNAs, particularly for in vivo or clinical applications.

Eenergy Extraction from air or Water by Vibrations

Eenergy Extraction from air or Water by VibrationsThe paper considers the possibility to derive energy from air or water in a non-traditional way (without using rotating equipment). For this purpose, the authors studied variations in the additional area of a vibrating object in a definite sequence found as the solution of an optimisation problem. In the work, stably moving mechatronic systems were synthesised and modelled, whose control is very simple (not requiring calibration), being a function of the changing sign of phase coordinates.

Duality for massive spin two theories in arbitrary dimensions

Using the parent Lagrangian approach we construct a dual formulation, in the sense originally proposed by Curtright and Freund, of a massive spin two Fierz-Pauli theory in arbitrary dimensions D. This is achieved in terms of a mixed symmetry tensor TA[B1B2...BD−2], without the need of auxiliary fields. The relation of this method with an alternative formulation based on a gauge symmetry principle proposed by Zinoviev is elucidated. We show that the latter formulation in four dimensions, with a given gauge fixing together with a definite sequence of auxiliary fields elimination via their equations of motion, leads to the parent Lagrangian already considered by West completed by a Fierz-Pauli mass term, which in turns yields the Curtright-Freund action. This motivates our generalization to arbitrary dimensions leading to the corresponding extension of the four dimensional result. We identify the transverse true degrees of freedom of the dual theory and verify that their number is in accordance with those of the massive Fierz-Pauli field.

Intracellular lipid droplet targeting by apolipoprotein A-V requires the carboxyl-terminal segment

The expression of apolipoprotein A-V (apoA-V) in hepatoma cells results in homing of this protein to intracellular lipid droplets. When hepatoma cells transfected with a full-length apoA-V-green fluorescent protein fusion protein were cultured in medium that was not supplemented with oleic acid (OA), intracellular lipid droplet size and number were reduced compared with those of cells supplemented with OA. Confocal microscopy studies revealed that apoA-V associates with lipid droplets under both conditions. To define the structural requirements for apoA-V lipid droplet association, hepatoma cells were transfected with a series of C-terminal truncated apoA-V variants. Confocal microscopy analysis revealed that, in a manner similar to mature full-length apoA-V (343 amino acids), truncation variants apoA-V(1-292), apoA-V(1-237), and apoA-V(1-191) associated with lipid droplets, while apoA-V(1-146) did not. Western blot analysis of the relative abundance of apoA-V in cell lysates versus conditioned medium indicated that apoA-V variants associated with lipid droplets were poorly secreted while apoA-V(1-146) was efficiently secreted. Ultracentrifugation of conditioned medium revealed that, unlike full-length apoA-V, which associates with lipoproteins, apoA-V(1-146) was present solely in the lipoprotein-deficient fraction. Deletion of the N-terminal signal peptide from apoA-V resulted in an inability of the protein to be secreted into the medium, although it associated with lipid droplets. Taken together, these data suggest that the C terminus of apoA-V is essential for lipid droplet association in transfected hepatoma cells and lipoprotein association in conditioned medium while the signal peptide is required for extracellular trafficking of this protein.

The rational exploration of microbial diversity

The exploration of the microbial world has been an exciting series of unanticipated discoveries despite being largely uninformed by rational estimates of the magnitude of task confronting us. However, in the long term, more structured surveys can be achieved by estimating the diversity of microbial communities and the effort required to describe them. The rates of recovery of new microbial taxa in very large samples suggest that many more taxa remain to be discovered in soils and the oceans. We apply a robust statistical method to large gene sequence libraries from these environments to estimate both diversity and the sequencing effort required to obtain a given fraction of that diversity. In the upper ocean, we predict some 1400 phylotypes, and a mere fivefold increase in shotgun reads could yield 90% of the metagenome, that is, all genes from all taxa. However, at deep ocean, hydrothermal vents and diversities in soils can be up to two orders of magnitude larger, and hundreds of times the current number of samples will be required just to obtain 90% of the taxonomic diversity based on 3% difference in 16S rDNA. Obtaining 90% of the metagenome will require tens of thousands of times the current sequencing effort. Although the definitive sequencing of hyperdiverse environments is not yet possible, we can, using taxa-abundance distributions, begin to plan and develop the required methods and strategies. This would initiate a new phase in the exploration of the microbial world.

Initiation of Mammalian O-Mannosylation in Vivo Is Independent of a Consensus Sequence and Controlled by Peptide Regions within and Upstream of the α-Dystroglycan Mucin Domain

To reveal insight into the initiation of mammalian O-mannosylation in vivo, recombinant glycosylation probes containing sections of human alpha-dystroglycan (hDG) were expressed in epithelial cell lines. We demonstrate that O-mannosylation within the mucin domain of hDG occurs preferentially at Thr/Ser residues that are flanked by basic amino acids. Protein O-mannosylation is independent of a consensus sequence, but strictly dependent on a peptide region located upstream of the mucin domain. This peptide region cannot be replaced by other N-terminal peptides, however, it is not sufficient to induce O-mannosylation on a structurally distinct mucin domain in hybrid constructs. The presented in vivo evidence for a more complex regulation of mammalian O-mannosylation contrasts with a recent in vitro study of O-mannosylation in human alpha-dystroglycan peptides indicating the existence of an 18-meric consensus sequence. We demonstrate in vivo that the entire region p377-417 is necessary and sufficient for O-mannosylation initiation of hDG, but not of MUC1 tandem repeats. The feature of a doubly controlled initiation process distinguishes mammalian O-mannosylation from other types of O-glycosylation, which are largely controlled by structural properties of the substrate positions and their local peptide environment.

Time resolved X-ray diffraction observations of phase transformations in transient arc welds

In situ X-ray diffraction methods have been developed at Lawrence Livermore National Laboratory for direct observation of microstructural evolution under quasi-steady state and transient welding conditions. Using intense highly collimated synchrotron radiation, the crystal structures in the weld heat affected and fusion zones are probed in real time to monitor solidification and solid state phase transformations during welding. Here the authors review recent work on the development and use of the time resolved X-ray diffraction (TRXRD) technique during transient welding and illustrate its unique capabilities to: directly observe the solidification mode; discover, in real time, the definitive sequence of phase transformations that lead to the final microstructure; and provide quantitative kinetic data of phase transformations through synthesis of TRXRD data with the temperature history obtained through heat transfer modelling. The TRXRD technique has been used to investigate welding induced phase transformations in titanium alloys, low alloy steels, and stainless steel alloys. The results show some of the first real time observations of the weld solidification mode and the evolution of equilibrium and non-equilibrium phases during rapid heating and cooling. When combined with numerical modelling, quantitative phase transformation kinetic data are obtained, allowing for its use in a wide variety of isothermal and non-isothermal processing. The potential for future applications of this and similar techniques is also addressed.

Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping.

BackgroundThe publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since the microchromosomes are notably under-represented. In an effort to develop maps for the microchromosomes absent from the chicken genome assembly, we developed radiation hybrid (RH) and genetic maps with markers isolated from sequence currently assigned to "chromosome Unknown" (chrUn). The chrUn is composed of sequence contigs not assigned to named chromosomes. To identify and map sequence belonging to the microchromosomes we used a comparative mapping strategy, and we focused on the small linkage group E26C13.ResultsIn total, 139 markers were analysed with the chickRH6 panel, of which 120 were effectively assigned to the E26C13 linkage group, the remainder mapping elsewhere in the genome. The final RH map is composed of 22 framework markers extending over a 245.6 cR distance. A corresponding genetic map was developed, whose length is 103 cM in the East Lansing reference population. The E26C13 group was assigned to GGA25 (Gallus gallus chromosome 25) by FISH (fluorescence in situ hybridisation) mapping.ConclusionThe high-resolution RH framework map obtained here covers the entire chicken chromosome 25 and reveals the existence of a high number of intrachromosomal rearrangements when compared to the human genome. The strategy used here for the characterization of GGA25 could be used to improve knowledge on the other uncharacterized small, yet gene-rich microchromosomes.

Clonal mutations in primary human glial tumors: evidence in support of the mutator hypothesis.

BackgroundA verifiable consequence of the mutator hypothesis is that even low grade neoplasms would accumulate a large number of mutations that do not influence the tumor phenotype (clonal mutations). In this study, we have attempted to quantify the number of clonal mutations in primary human gliomas of astrocytic cell origin. These alterations were identified in tumor tissue, microscopically confirmed to have over 70% neoplastic cells.MethodsRandom Amplified Polymorphic DNA (RAPD) analysis was performed using a set of fifteen 10-mer primers of arbitrary but definite sequences in 17 WHO grade II astrocytomas (low grade diffuse astrocytoma or DA) and 16 WHO grade IV astrocytomas (Glioblastoma Multiforme or GBM). The RAPD profile of the tumor tissue was compared with that of the leucocyte DNA of the same patient and alteration(s) scored. A quantitative estimate of the overall genomic changes in these tumors was obtained by 2 different modes of calculation.ResultsThe overall change in the tumors was estimated to be 4.24% in DA and 2.29% in GBM by one method and 11.96% and 6.03% in DA and GBM respectively by the other. The difference between high and lower grade tumors was statistically significant by both methods.ConclusionThis study demonstrates the presence of extensive clonal mutations in gliomas, more in lower grade. This is consistent with our earlier work demonstrating that technique like RAPD analysis, unbiased for locus, is able to demonstrate more intra-tumor genetic heterogeneity in lower grade gliomas compared to higher grade. The results support the mutator hypothesis proposed by Loeb.

SATB1-binding sequences and Alu-like motifs define a unique chromatin context in the vicinity of human immunodeficiency virus type 1 integration sites.

Retroviral integration has recently been shown to be nonrandom, favoring transcriptionally active regions of chromatin. However, the mechanism for integration site selection by retroviruses is not clear. We show here the occurrence of Alu-like motifs in the sequences flanking the reported viral integration sites that are significantly different from those obtained from the randomly picked sequences from the human genome, suggesting that unique primary sequence features exist in the genomic regions targeted by human immunodeficiency virus type 1 (HIV-1). Additionally, these sequences were preferentially bound by SATB1, the T lineage-restricted chromatin organizer, in vitro and in vivo. Alu repeats make up nearly 10% of the human genome and have been implicated in the regulation of transcription. To specifically isolate sequences flanking the viral integration sites and also harboring both Alu-like repeats and SATB1-binding sites, we combined chromatin immunoprecipitation with sequential PCRs. The cloned sequences flanking HIV-1 integration sites were specifically immunoprecipitated and amplified from the pool of anti-SATB1-immunoprecipitated genomic DNA fragments isolated from HIV-1 NL4.3-infected Jurkat T-cell chromatin. Moreover, many of these sequences were preferentially partitioned in the DNA associated tightly with the nuclear matrix and not in the chromatin loops. Strikingly, many of these regions were disfavored for integration when SATB1 was silenced, providing unequivocal evidence for its role in HIV-1 integration site selection. We propose that definitive sequence features such as the Alu-like motifs and SATB1-binding sites provide a unique chromatin context in vivo which is preferentially targeted by the HIV-1 integration machinery.