Map Fixes Gta 5

[Crispina Blomker]

Weuse the term backporting to describe the action of taking a fix for a security flaw out of the most recent version of an upstream software package and applying that fix to an older version of the package we distribute.

Backporting is common among vendors like Red Hat and is essential to ensuring we can deploy automated updates to customers with minimal risk. Backporting might be a new concept for those more familiar with proprietary software updates.

Red Hat provides version 5.3 of PHP in Red Hat Enterprise Linux 6. The upstream version of PHP 5.3 has reached the end of life on August 14, 2014, meaning that no additional fixes or enhancements are provided for this version by upstream. However, on October 14, 2014, a buffer overflow flaw CVE-2014-3670, rated as Important, has been discovered in all versions of PHP that could allow a remote attacker to crash a PHP application or, possibly, execute arbitrary code with the privileges of the user running that PHP application.

Because version 5.3 of PHP has been retired upstream, the fix for this issue was not provided in an upstream release of PHP 5.3. The only way to mitigate the issue would be to upgrade to PHP 5.4, which did provide a fix for CVE-2014-3670. However, Red Hat customers using PHP 5.3 may not be able to migrate to PHP 5.4 due to possible backward compatibility problems between versions 5.3 and 5.4. The migration process would require manual effort by system administrators or developers. For this reason, Red Hat provided (backported) the fix for this issue to the PHP 5.3 packages shipped with Red Hat Enterprise Linux 6 so that customers could keep using PHP 5.3 and would mitigate CVE-2014-3670 at the same time.

For most products, our default practice is to backport security fixes, but we do sometimes provide version updates for some packages after careful testing and analysis. These are likely to be packages that have no interaction with others, or those used by an end-user, such as web browsers and instant messaging clients.

Backporting has a number of advantages for customers, but it can create confusion when it is not understood. Customers need to be aware that just looking at the version number of a package will not tell them if they are vulnerable or not. For example, stories in the press may include phrases such as "upgrade to Apache httpd 2.0.43 to fix the issue," which only takes into account the upstream version number. This can cause confusion as even after installing updated packages from a vendor, it is not likely customers will have the latest upstream version. They will instead have an older upstream version with backported patches applied.

Also, some security scanning and auditing tools make decisions about vulnerabilities based solely on the version number of components they find. This results in false positives as the tools do not take into account backported security fixes.

Since the introduction of Red Hat Enterprise Linux, we have been careful to explain in our security advisories how we fixed an issue, whether by moving to a new upstream version or by backporting patches to the existing version. We have attached CVE names to all our advisories since January 2000, allowing customers to easily cross-reference vulnerabilities and find out how and when we fixed them, independent of version numbers.

We also supply OVAL definitions (machine-readable versions of our advisories) that third-party vulnerability tools can use to determine the status of vulnerabilities, even when security fixes have been backported. In doing this, we hope to remove some of the confusion surrounding backporting and make it easier for customers to always keep up to date with the latest security fixes.

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Nitrogen is an essential component of all living organisms and limits life in the ocean. Atmospheric N2 gas is the largest reservoir of freely accessible nitrogen, but it is biologically available only to microorganisms that carry the nitrogenase metalloenzyme and thus can fix N2 into ammonia7. Even though a wide diversity of marine bacteria and archaea encode nitrogenase, the bulk of nitrogen fixation in the ocean has been attributed to cyanobacteria (ref. 4 and references therein). These phototrophs are capable of both free-living and symbiotic lifestyles, and can directly or indirectly contribute to carbon fixation and export production in the regions where they are abundant, such as oligotrophic coastal waters and margins of subtropical gyres8. Notably, in vast regions of the ocean, such as the centres of subtropical gyres, cyanobacterial N2 fixers are too rare to account for the measured rates of N2 fixation. Instead, a role of non-cyanobacterial N2 fixers has been invoked, on the basis of the abundance of nitrogenase-encoding gene sequences (nifH), most of which belong to uncultured proteobacteria (for example, refs. 3,5,9,10,11). So far, the most frequently detected non-cyanobacterial N2 fixer is the so-called gamma-A, named after its nifH gene phylogeny that clusters within the Gammaproteobacteria12. This enigmatic microorganism has been shown to be distributed in most world oceans, and its potential activity has been inferred from in situ nifH transcription13,14. To date, however, there is no proof that gamma-A fixes N2 in situ, and essentially all aspects of its physiology remain unknown.

Notably, Ca. T. diatomicola seems to have lost its low-affinity terminal oxidase (Supplementary Table 1), which is typically present in other members of the Hyphomicrobiaceae family, with the notable exception of Ca. T. profundi (Supplementary Table 3). Instead, Ca. T. diatomicola encodes and highly transcribes the high-affinity cytochrome cbb3-type (ccoN, ccoO and ccoP) terminal oxidase (Fig. 2a, Extended Data Fig. 6 and Supplementary Table 1), which is used for respiration under low-oxygen conditions, and is generally poorly transcribed in high-oxygen environments such as the oxic surface waters of the tropical North Atlantic32. Legume-associated N2-fixing rhizobia also rely on high-affinity terminal oxidases when growing symbiotically29, because the plant hosts restrict the oxygen supply to the symbionts to control their growth and optimize nitrogen fixation33. The legume hosts also suppress the activity of the AMT-type ammonium transporters of nodulating rhizobia, to prevent the uptake of ammonium by the bacteria and to enhance ammonium transfer to the plant30. The lack of AMT transporters in Ca. T. diatomicola would similarly maximize the transfer of ammonia to the Haslea host. Ca. T. diatomicola seems to lack the capacity for de novo biosynthesis of some essential amino acids (aromatic amino acids, histidine and proline) and vitamins (for example, biotin and thiamine; Supplementary Table 1), a trait also found in nodulating Rhizobiales that are dependent on their plant host for these essential compounds34,35. Together, these results indicate that, similarly to nodulating rhizobia in legume symbioses, growth and N2 fixation by Ca. T. diatomicola is tightly regulated by its host.

Because the Hyphomicrobiaceae evolved more than 1,000 million years ago, well before nodulating Rhizobiales lineages began to form symbioses with legume plants around 100 million years ago17,18, we speculate that beneficial N2-fixing symbioses in the Rhizobiales order evolved independently in marine environments much earlier than the nodulating species on land. Although Ca. T. diatomicola and the nodulating Rhizobiales evolved from one common ancestor and have similar metabolic interactions with their hosts, different degrees of host dependency have resulted in different evolutionary genome adaptations. The terrestrial nodulating rhizobial lineages form facultative symbioses with their host, and have undergone genome expansion to accommodate both a free-living and an intracellular lifestyle18. By contrast, the marine Ca. T. diatomicola has strongly reduced its genome size, in line with its proposed obligate symbiotic lifestyle. As such, the evolutionary adaptations of Ca. T. diatomicola are similar to those of the endosymbiotic cyanobacterium UCYN-A, which functions as an early-stage N2-fixing organelle37. It is tempting to speculate that Ca. T. diatomicola, which fulfils the same function in diatoms as UCYN-A does in haptophyte algae, is also in the early stages of becoming an N2-fixing organelle. This raises the possibility that endosymbiosis-derived N2-fixing organelles have originated not only from the cyanobacteria, but also from the Rhizobiales.

Nitrogen-fixing symbiotic Rhizobiales are crucial players in terrestrial productivity; they enable legumes to produce biomass through photosynthesis and consequently provide 20% of the proteins in food production (ref. 7 and references therein). Our results show that symbiotic marine N2-fixing Rhizobiales, such as Ca. T. diatomicola, are major contributors to oceanic N2 fixation and have a crucial role in sustaining marine productivity and global CO2 sequestration.

Samples from a total of eight stations were selected for DNA and RNA extractions and subsequent long- and short-read metagenomic and metatranscriptomic sequencing. All library preparation steps and sequencing were performed at the Max Planck Genome Centre ( ). See Supplementary Methods for details of samples, DNA and RNA extraction protocols, library preparation for short- and long-read sequencing and quality trimming.

To obtain gene transcription information for Ca. T. diatomicola, all sequenced metatranscriptome reads were combined and mapped to the Ca. T. diatomicola genome using BWA-MEM61 v.0.7.17-r1188, and the resulting mapping files were filtered requiring at least 95% sequence identity and at least 80% of the read to align (mapping and filtering were done through CoverM v.0.6.1). Gene counts were generated using featureCounts62 v.2.0.1 and TPM values for protein-coding genes were calculated as previously described63. The genome plot (Fig. 2a) including TPM values was generated using BRIG64 v.0.95 and DNAPlotter65 v.18.1.0.

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