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What is an isolated beta bridge?

What is an isolated beta bridge?


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DSSP gives the letter B for a "residue in isolated β-bridge (single pair β-sheet hydrogen bond formation)", according to Wikipedias page for secondary structure (and various other proper sources). Can somebody please explain what this is in some more detail please? If I google it all that comes up is pretty much the same as what wikipedia gives.


In Kabash and Sander's paper related to DSSP (Biopolymers 1983 vol. 22 (12) pp. 2577-637) the following appears in the abstract:

We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.”

It seems from this that they are using the term bridge to mean one hydrogen bond of the type found in a beta-sheet, ladder as two protein strands joined by many hydrogen bonds, and sheets as beta-sheets - more than two protein strands joined by many hydrogen bonds. The term beta-bridge in the DSSP documentation (http://www.cmbi.ru.nl/dssp.html) is presumably equivalent to a bridge in the paper

In the DSSP files residues that are in ladders or beta-sheets are designated E, and B is used for instances where there is a single hydrogen bond. The former are very common, wheres the latter are quite rare - some proteins have none. I have prepared an image of an example for residues 74 and 79 (side-chains omitted for clarity) in a loop in the protein 1PPR.pdb (a light-harvesting protein). The other loop residues 75-78 are designated as T (turn) in the DSSP file, whereas residues 73 and 78 have no structure designation. Hence the hydrogen bond between Ser-74 and Val-79 is an isolated singleton and designated B.


Lab 14: Isolation and Identification of Streptococci

There are two genera of bacteria that can appear as a streptococcus arrangement that we will take up in the lab: the genus Streptococcus and the genus Enterococcus. Both are Gram-positive cocci 0.5-1.0 µm in diameter, typically occurring in pairs and chains of varying length when grown in a liquid medium, and often occurring singly, in pairs, short chains, and clusters when taken from an agar culture. As learned in Lab 8, they are both catalase-negative.

A. The genus Streptococcus

Streptococcus species are usually classified clinically based on their hemolytic properties on blood agar and according to their serologic groups.

  • Scanning electron micrograph Streptococcus pyogenes courtesy of Dennis Kunkel's Microscopy .
  • Transmission electron micrograph of Streptococcus from the Rockefeller University web page.
  • Scanning electron micrograph of a Streptococcus pneumoniae.

The streptococci are usually isolated on Blood agar. Blood agar is one of the most commonly used media in a clinical lab. It consists of an enriched agar base (Tryptic Soy agar) to which 5% sheep red blood cells have been added. Blood agar is commonly used to isolate not only streptococci, but also staphylococci and many other pathogens. Besides providing enrichments for the growth of fastidious pathogens, Blood agar can be used to detect hemolytic properties.

Hemolysis refers to is the lysis of the red blood cells in the agar surrounding bacterial colonies and is a result of bacterial enzymes called hemolysins. Although hemolysis can often be observed with the naked eye, ideally it should be examined microscopically using low power magnification, especially in cases of doubtful hemolysis. Reactions on blood agar are said to be beta, alpha, gamma, or double-zone:

1. Beta hemolysis (see Fig. 1A and Fig. 1B)refers to a clear, red blood cell-free zone surrounding the colony, where a complete lysis of the red blood cells by the bacterial hemolysins has occurred. This is best seen in subsurface colonies where the agar has been stabbed since some bacterial hemolysins, like streptolysin O, are inactivated by oxygen.

2. Alpha hemolysis (see Fig. 5A and Fig. 5B) appears as a zone of partial hemolysis surrounding the colony, often accompanied by a greenish discoloration of the agar. This is also best seen in subsurface colonies where the agar has been stabbed.

3. Gamma reaction (see Fig. 6) refers to no hemolysis or discoloration of the agar surrounding the colony.

4. Double-zone hemolysis (see Fig. 10) refers to both a beta and an alpha zone of hemolysis surrounding the colony.

See Fig. 11 to view a photograph showing alpha, beta, and gamma hemolysis on blood agar.

See Fig. 12 for a blood agar plate of a throat culture showing possible Streptococcus pyogenes.

Many of the streptococci can also be classified under the Lancefield system. In this case, they are divided into 19 different serologic groups on the basis of carbohydrate antigens in their cell wall. These antigenic groups are designated by the letters A to H, K to M, and O to V. Lancefield serologic groups A, B, C, D, F, and G are the ones that normally infect humans, however, not all pathogenic streptococci can be identified by Lancefield typing (e.g., Streptococcus pneumoniae). Serologic typing to identify microorganisms will be discussed in more detail later in Lab 17. Single-stranded DNA probes complementary to species-specific r-RNA sequences of streptococci and enterococci are also being used now to identify these organisms.


Classification

Based on the reducing power, disaccharides are classified into two categories.

Reducing Disaccharides

They can act as reducing agents and can donate electrons to the recipients in the redox reaction. In these disaccharides, one of the monosaccharides retains its free functional group that can participate in the redox reaction. The functional group of only one monosaccharide is consumed in the formation of the glycosidic bond. An example of reducing disaccharide is maltose.

Non-reducing Disaccharides

These disaccharides do not behave as a reducing agent because they do not have a free aldehydic or ketonic functional group. The functional groups of both the monosaccharides are consumed in the process of glycosidic bond formation. Sucrose is an example of a non-reducing disaccharide.


The api provided to exposeInMainWorld must be a Function , String , Number , Array , Boolean , or an object whose keys are strings and values are a Function , String , Number , Array , Boolean , or another nested object that meets the same conditions.

Значения Function передаются в другой контекст, а все остальные значения копируются и заморожены. Any data / primitives sent in the API become immutable and updates on either side of the bridge do not result in an update on the other side.

An example of a complex API is shown below:

Функции API

Значения Function , которые вы связываете через contextBridge , передаются через Electron, чтобы гарантировать, что контексты остаются изолированными. Это приводит к некоторым ключевым ограничениям, которые мы описали ниже.

Параметр / Ошибка / Поддержка возвращаемого типа

Because parameters, errors and return values are copied when they are sent over the bridge, there are only certain types that can be used. At a high level, if the type you want to use can be serialized and deserialized into the same object it will work. Ниже для полноты изложения приводится таблица поддержки типов:

ТипСложностьПоддержка параметровВозврат значения поддержкиОграничения
String ПростойНет
Number ПростойНет
Boolean ПростойНет
Object СложныйKeys must be supported using only "Simple" types in this table. Значения должны поддерживаться в этой таблице. Модификации прототипа отбрасываются. Отправка пользовательских классов будет копировать значения, но не прототип.
Array СложныйТе же ограничения, что и в типе Object
Error СложныйОшибки, которые выбрасываются также копируются, это может привести к тому, что сообщение и трассировка стека ошибки немного изменятся из-за того, что они будут выброшены в другом контексте
Promise СложныйPromises are only proxied if they are the return value or exact parameter. Promises nested in arrays or objects will be dropped.
Function СложныйМодификации прототипа отбрасываются. Отправка классов или конструкторов не будет работать.
Cloneable TypesПростойСмотрите связанный документ по клонируемым типам
Element СложныйМодификации прототипа отбрасываются. Sending custom elements will not work.
Symbol НетСимволы не могут быть скопированы в разных контекстах, поэтому они отбрасываются

If the type you care about is not in the above table, it is probably not supported.

Exposing Node Global Symbols

The contextBridge can be used by the preload script to give your renderer access to Node APIs. The table of supported types described above also applies to Node APIs that you expose through contextBridge . Please note that many Node APIs grant access to local system resources. Be very cautious about which globals and APIs you expose to untrusted remote content.

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Find a Specialist Find a Specialist

If you need medical advice, you can look for doctors or other healthcare professionals who have experience with this disease. You may find these specialists through advocacy organizations, clinical trials, or articles published in medical journals. You may also want to contact a university or tertiary medical center in your area, because these centers tend to see more complex cases and have the latest technology and treatments.

If you can’t find a specialist in your local area, try contacting national or international specialists. They may be able to refer you to someone they know through conferences or research efforts. Some specialists may be willing to consult with you or your local doctors over the phone or by email if you can't travel to them for care.

You can find more tips in our guide, How to Find a Disease Specialist. We also encourage you to explore the rest of this page to find resources that can help you find specialists.

Healthcare Resources

  • To find a medical professional who specializes in genetics, you can ask your doctor for a referral or you can search for one yourself. Online directories are provided by the American College of Medical Genetics and the National Society of Genetic Counselors. If you need additional help, contact a GARD Information Specialist. You can also learn more about genetic consultations from MedlinePlus Genetics.

Polysaccharide Structure

Polysaccharides form when monosaccharides or disaccharides link together by glycosidic bonds. The sugars participating in the bonds are called residues. The glycosidic bond is a bridge between the two residues consisting of an oxygen atom between two carbon rings. The glycosidic bond results from a dehydration reaction (also termed a condensation reaction). In the dehydration reaction a hydroxyl group is lost from a carbon of one residue while a hydrogen is lost from a hydroxyl group from another residue. A water molecule (H2O) is removed and the carbon of the first residue joins to the oxygen from the second residue.

Specifically, the first carbon (carbon-1) of one residue and the fourth carbon (carbon-4) of the other residue are linked by the oxygen, forming the 1,4 glycosidic bond. There are two types of glycosidic bonds, based on the stereochemistry of the carbon atoms. An α(1→4) glycosidic bond forms when the two carbon atoms have the same stereochemistry or the OH on carbon-1 is below the sugar's ring. A β(1→4) linkage forms when the two carbon atoms have different stereochemistry or the OH group is above the plane.

The hydrogen and oxygen atoms from residues form hydrogen bonds with other residues, potentially resulting in extremely strong structures.


Contents

Ancient Ruins sites have so far been found to have three main topographical configurations, each of which has multiple minor variations in how alien structures like obelisks are arranged.

  • Alpha layouts - 4 identified variants. All Alpha-type sites have the first third of Guardian data entries.
  • Beta layouts - 5 identified variants. All Beta-type sites have the second third of Guardian data entries.
  • Gamma layouts - 3 identified variants. All Gamma-type sites have the final third of Guardian data entries.

Колорадский университет в Боулдере

CU-Boulder is a dynamic community of scholars and learners on one of the most spectacular college campuses in the country. As one of 34 U.S. public institutions in the prestigious Association of American Universities (AAU), we have a proud tradition of academic excellence, with five Nobel laureates and more than 50 members of prestigious academic academies.


What is bioinformatics?

Put simply, bioinformatics is the science of storing, retrieving and analysing large amounts of biological information. It is a highly interdisciplinary field involving many different types of specialists, including biologists, molecular life scientists, computer scientists and mathematicians.

The term bioinformatics was coined by Paulien Hogeweg and Ben Hesper to describe “the study of informatic processes in biotic systems” and it found early use when the first biological sequence data began to be shared. Whilst the initial analysis methods are still fundamental to many large-scale experiments in the molecular life sciences, nowadays bioinformatics is considered to be a much broader discipline, encompassing modelling and image analysis in addition to the classical methods used for comparison of linear sequences or three-dimensional structures (Figure 1).

Figure 1 A broad overview of the different types of data that fall within the scope of bioinformatics. Traditionally, bioinformatics was used to describe the science of storing and analysing biomolecular sequence data, but the term is now used much more broadly, encompassing computational structural biology, chemical biology and systems biology (both data integration and the modelling of systems).

Distinction from medical informatics

Bioinformatics is distinct from medical informatics – the interdisciplinary study of the design, development, adoption and application of IT-based innovations in healthcare services delivery, management and planning. Somewhere in between the two disciplines lies biomedical informatics – the interdisciplinary field that studies and pursues the effective uses of biomedical data, information, and knowledge for scientific enquiry, problem solving and decision making, motivated by efforts to improve human health.

Recently initiated projects, such as the 100,000 Genomes Project, are bridging the gaps between these disciplines, but on the whole bioinformatics deals with research data and uses it for research purposes, medical informatics deals with data from individual patients for the purposes of clinical management, (diagnosis, treatment, prevention…) and biomedical informatics attempts to bridge these two extremes.


EXPLAINED: What Is The Delta-plus Variant That's Emerged As A Covid Worry While Experts Warn Of A Third Wave

As experts warn of a third wave in India, attention has moved to the new Delta-plus variant of the novel coronavirus, which as yet has been detected only in a very small number of cases in the country. But given how the Delta variant, or B.1.617.2, of the novel coronavirus fuelled the second wave of cases in the country, authorities will be tracking this new variant, also called AY.1, closely. Here’s what you need to know.

Did The Delta-plus Variant Emerge In Nepal?

Reports say that the first samples of this variant were isolated in Europe in March. Then, health authorities in England said in a briefing earlier this month that the first five cases sequenced in the country, in end-April, “were contacts of individuals who had travelled from, or transited through, Nepal and Turkey".

Dr Jeff Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute, has been quoted as saying that the key mutation that marks out the Delta-plus variant from the original Delta variant — called the K417N mutation — was first identified in Nepal. “It has also been observed once in Nepal (which does very little sequencing), and 14 times in Japan, of which 13 are samples from airport quarantine from travellers from Nepal," Dr Barrett has said.

Delta Plus Variant FAQ: States on Alert, Centre & Global View, Questions on Vaccines' 'Losing Efficacy'

Coronavirus News LIVE Updates: Difficult to Say If Delta Plus Variant Creating Problems in India, Says AIIMS Dir

But WHO’s Nepal office tweeted on June 3 that they were “not aware of any new variant of SARS-CoV-2 being detected in Nepal. The 3 confirmed variants in circulation are: Alpha (B.1.1.7), Delta (B.1.617.2) and Kappa (B.1.617.1). The predominant variant currently in circulation in Nepal is Delta (B.1.617.2)."

The Centre has said that as of now, Delta-plus is not a variant of concern for India and neither has it got that billing from the World Health Organisation (WHO). Dr VK Paul, Member (Health), NITI Aayog, said that “its presence had been detected and submitted to global data system".

So, What Is Delta-plus? How Is It Different From The Delta Variant?

The B.1.617 lineage that gave us the Variant of Concern called Delta (B.1.617.2) and the Variant of Interest called Kappa (B.1.617.1) apart from the B.1.617.3, another variant that’s also being monitored. The Delta-plus variant, as the name suggests, is a modification on the B.1.617.2 Delta variant. The novel coronavirus has been busy taking on mutations, which are nothing but slight changes in the genetic composition of the virus.

Every time these mutations change the way that the virus behaves, a new variant of the virus is said to emerge. The Delta variant, also called the ‘double mutant’ variant, was seen as being more infectious because it had two key mutations, called E484Q and L452R.

Now, the Delta-plus variant has been found to exhibit the K417N mutation. According to The New York Times, the K417N, along with another mutation called K417T, is a mutation in the spike protein of the novel coronavirus.

The spikes on its surface, which give the coronavirus its name, also helps the virus to invade human cells.

Reports say that the “mutation appears on the tip of the coronavirus spike, and may help the virus bind more tightly to human cells".

But Delta-plus is not the only variant which carries this mutation. Two other WHO-designated Variants of Concern, the Beta, or B.1.351 first seen in South Africa, and the Gamma, or P.1 variant first seen in Brazil, both have the K417N mutation. Surprisingly though, the B.1.617.2 Delta variant doesn’t carry this mutation.

How Serious Is The Risk Posed By Delta-plus? Are Vaccines Effective Against It?

Sharing preliminary details of the Delta-plus variant, researchers at CSIR- Institute of Genomics and Integrative Biology (IGIB) said that it may be linked with abilities to better escape immune response, which means the virus can potentially dodge vaccines and antibody therapies. In fact, Vinod Scaria, a scientist with IGIB, said that there is also evidence of Delta-plus variant’s “resistance to monoclonal antibodies Casirivimab and Imdevimab". The reference is to the monoclonal antibody cocktail that was recently okayed for treatment of milder cases of Covid-19 in India.

As to the question whether vaccines are effective against this variant, UK health officials reported that of the 36 Delta-plus cases identified till early June, at least 18 were not vaccinated. Among the people who were vaccinated, only 2 were those who had received both shots and more than 14 days had passed between the second dose and the positive test. Importantly, “no deaths have been recorded amongst the 36 cases," the health officials said.

Where Has The Delta-plus Variant Spread?

Health officials in England said that till June 7, 63 Delta-plus genomes had been identified on the GISAID worldwide repository. Of these six were from India, nine from Poland, 12 from Portugal and 14 from the US.

Giving the age break-up of Delta-plus cases in England, health officials said that the majority were in younger individuals, with only two of the 36 Delta-plus cases in people aged above 60 years. Further, 11 of the cases were travel related (six travellers and five cases amongst contacts of travellers) while 12 cases had no history of travel or contact with travellers. The countries related to Delta-plus cases, according to English officials, “may include direct travel from or transit through" among others, India, Malaysia, Nepal, Singapore and Turkey.