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 Microbiology: Identification of microbial gene products with biological activity in inflammatory bowel disease

Christopher Huttenhower and colleagues now report a generalizable computational platform for the identification and characterization of putatively biologically active microbial products from metagenomic datasets, which they use to detect immune-active microbial products that may play a functional role in the pathogenesis of inflammatory bowel disease (IBD).

ABSOLUTE READINGS

The instrument shows the actual value

without compensating to a reference

temperature.

AC-ADAPTOR

An internationally approved mains-plug

with built-in low voltage transformer for

a safe supply of energy to instruments.

ACCURACY

Maximum electronic error of the

measured unit. The accuracy of an

electrochemical determination such as

pH, conductivity, dissolved oxygen &

ion-selective measurements is mainly

limited by the electrodes and calibration

solutions.

ALARM

An alert sounds or a relay is closed

when readings stray outside pre-set

limits.

ALTERNATING DISPLAY

The meter can automatically scan

all selected inputs for display or

transmission to a computer or printer.

AUTOMATIC CROSS-OVER

When the resistance of an

electrophoresis apparatus changes

during a run, the power supply is able to

switch automatically between constant

voltage, constant current and constant

power.

BATTERY CAPACITY

Percentage of remaining battery

capacity.

BAUD RATE

Communication speed, in bits/second

(b/s), of the digital interface (RS232).

BUFFER

A solution of buffered species where the

pH tends to remain constant if diluted or

concentrated.

Pre-programmed pH buffers: 1.68/ 2.00/

4.00/ 4.01/ 6.87/ 7.00/ 9.18/ 9.21/ 10.01/

12.00/ 12.45.

User specified pH buffers: special tables

can be stored for future calibrations.

CALIBRATION REMINDER

A timed calibration procedure facilitates

considerably GLP management by

prompting the user when his instrument

needs to be recalibrated.

CAPACITIVE COMPENSATION

The capacity of the electrode and its

cable falsifies the measurement at

very low conductivities. A capacity

compensation allows to compensate for

these errors.

CELL

The 2-pole design is the most

commonly used conductivity cell. The

electrodes are made of platinised

platinum. The cell must be replaced

or re-platinised if the plates become

fouled.

The 4-pole design reduces considerably

the problems of polarisation and fouling.

By utilising four electrodes, no current

flows through the measuring circuit. The

AC-current is only applied to the outer

pair of rings allowing the inner pair

of electrodes to measure the voltage

without any polarisation effects.

CELL CONSTANT

The cell constant (cm-1) of a

conductivity electrode is determined by

the length (cm) of the column of liquid

between the plates divided by the area

(cm2) of the plates.

CONCENTRATION

Concentration measurement with an ion

selective electrode requires a minimum

of chemical know-how to make

successful ion selective determinations.

CONDUCTIVITY

The conductivity is a measure of the

solution’s ability to conduct electric

current. The basic unit is Siemens/cm

(S/cm). It is measured by an electrode

consisting of two platinum plates

to which an alternating potential is

applied. The corresponding current is

proportional to the conductivity of the

ionic solution in which the electrode is

dipped.

DATA-ACQUISITION

Connect the instrument to a computer

via an USB, RS232, RS485 interface

for bi-directional communication

capabilities. Most instruments require

no special software and feature an

advanced easy to use data acquisition

fully compatible with spread-sheet.

DATA-LOGGING

Stores automatically or manually the

measured values (+ °C & time/date) in

a built-in non-volatile memory.

GLP

Good Laboratory Practices procedures

help to increase accuracy through

calibration reports.

GROUND LEAKAGE

Leaking or dirty electrophoresis

apparatus are dangerous, since the

applied high voltage may result in an

electric current flowing through the

operator to the ground.

IDENTIFICATION NUMBER

Several instruments connected to the

same computer can easily be identified

when specific numbers are allocated to

them.

INPUT

Several types of connectors are used

according to the application. Check

the specifications of meter-input and

electrode-plug on their compatibility.

ISO-pH

Zero-point of a pH electrode. A new pH

electrode has an ISO-pH between 6.5

and 7.5 pH.

MINIMUM/MAXIMUM MEMORY

Recalls the lowest/highest values ever

measured since the last calibration.

mV

Electrode potential is read in mV.

ON/OFF CONTROL

Simple control system in which the

relays are continuously closed when a

pre-set level is exceeded.

ORP

Oxido-Reduction-Potential (the reducing

or oxidising capability of a solution).

PASSWORD PROTECTION

For tamper-proof storage of parameters

and data, a secret personal code

protects the instrument against any

undesired access.

pH

The pH is a measurement for the acidity

or alkalinity of a solution. In pure water

the hydrogen ion (H+) and hydroxyl

ion (OH-) concentrations are equal at

10-7 M (25°C). To provide a convenient

and effective means of defining acidity

and alkalinity, the negative logarithm of

hydrogen ion activity is used. The pH is

calculated from the potential between a

glass and a reference electrode (Nernst

equation).

PROPORTIONAL CONTROL

The control relay will pulse at a rate

proportional to the regulation difference.

When the difference is superior to

a pre-set maximum value, the relay

is continuously activated. However,

when reaching a pre-set level the waittime between the pulses will increase

gradually in order to perform very

accurate regulations.

Pt100

Platinum resistance thermometer (100

Ω at 0°C). It requires a low resistance

cable for highest accuracy.

Pt1000

Platinum resistance thermometer (1000

Ω at 0°C). Less errors when using

longer cables.

QUALITY MANAGEMENT

Measuring equipment should be

calibrated on a regular basis (GLP).

The accuracy of measurements is

only limited by the electrodes and

calibration solutions. At any moment,

a complete documentation about the

electrodes and calibration solutions can

be printed or sent to a computer. This

includes meter settings, data about the

last calibration and a comparison with

the previous calibration. The use of

certified calibration solutions is strongly

recommended. For very accurate

quality measurements fresh standard

solutions should be used for each

calibration.

Technical data

88

QUANTIFICATION OF VINCENT

The quantification of Vincent is a

measurement for the energy stored in

an organism. It expresses the maximum

dissipation of energy by a chemical or

biochemical reaction. The basic unit is

Watt (W) but it is more convenient to

use µW (micro-watt). It is calculated

from the ORP, referenced against a

hydrogen electrode, and the resistance.

RANGE LOCK

Allows to lock the initial conductivity

measuring range when titrating in

order to avoid cross-over errors due

to varying measuring frequencies and

linearity errors of the conductivity cell.

REAL TIME CLOCK

Shows time and date on the display.

REDOX POTENTIAL

The potential developed by a metallic

electrode when placed in a solution

containing a species in two different

oxidation states. It is usually measured

by a combination platinum electrode.

REFERENCE TEMPERATURE

Conductivity measurements are

temperature dependent. Therefore,

the readings should be referenced to a

standard temperature.

RESISTIVITY

Electrical resistivity is the reciprocal of

Conductivity. The basic unit is Ohm.

cm (Ω.cm). While the ion concentration

of a solution decreases, the resistivity

rises up to a maximum of 18.3 MΩ.cm

(absolute pure water at 25°C).

RESOLUTION

Smallest possible reading of the

measured unit. More sophisticated

meters allow to select the desired

resolution. Unlike other meters, the

CONSORT models round off the last

digit rather than simply truncating digits

outside the display range.

rH2

The rH2 is a measurement for the

level of electronic exchanges between

water and dissolved ions. It enables

to study incomplete, indeterminate

and very diluted aqueous redox

solutions. It is defined as the negative

logarithm of molecular hydrogen ion

activity, calculated from the pH and the

ORP referenced against a hydrogen

electrode.

RS232

Digital interface, transmits the displayed

values and calibration data to a printer

or computer.

RS485

Allows to connect several process

controllers for bi-directional

communication with a computer. It

allows multiple devices (up to 32) to

communicate at half-duplex on a single

pair of wires, plus a ground wire, at

distances up to 1200 meters.

SALINITY

Salinity gives an indication of the salt

content of sea water. It is calculated

from the conductivity referred to 15°C.

The salinity is the ratio between the

total salt content (g) and the total weight

of the sea water (kg). Hence salinity

can be expressed in ppt (parts per

thousand).

SLOPE

Percentage which relates the actual

behaviour of a pH electrode to the

Nernst’s law. A new electrode has a

slope between 95 and 100 %.

S/S RELAY

A solid-state relay contains no

mechanical contacts. Long life, compact

design and spark-free switching are its

main advantages. It should not be used

for controlling very low power loads, as

the small leakage current can cause

unwanted switching-on.

STABILITY INDICATION

A decimal point flashes until the

electrode output remains constant, then

readings can be recorded.

TDS

Total Dissolved Salts of a solution

gives an indication of the total ion

concentration. Due to ionic interactions

within a solution, the salt concentration

cannot easily be related to conductivity.

As the dissolved solids are generally

unknown, a TDS measurement is

always referred to a solution of pure

Sodium Chloride.

TEMPERATURE COEFFICIENT

Each solution has its own temperature

coefficient (%/K). As this coefficient also

varies with temperature, a standard

conductometer cannot achieve a

precise temperature compensation over

a wide span of temperatures. However,

a research grade meter is able to plot

special temperature curves for each

individual type of solutions in its nonvolatile memory. Specific temperature

coefficients can also be entered for

special applications. For standard

applications, the non-linear function for

natural waters (EN27888) is used.

TEMPERATURE COMPENSATION

Corrects readings for variations in

electrode response due to temperature

effects.

THERMOCOUPLE

Thermocouples basically consist of

two dissimilar wires (each made of a

different alloy). One end is twisted or

soldered to form a measuring junction.

The other end is connected to a

thermometer and forms the reference

junction. The signal is a small voltage

(μV) proportional to the temperature

gradient between the measuring and

reference junctions. Thermocouple

probes are ideal to cover greater

lengths. They also have a great

temperature range and can easily pass

through e.g. oven doors. Response

time is faster than with Pt100 probes.

Accuracy, stability and repeatability are

less than with Pt100 probes.

USB

Universal Serial Bus is a standard

designed to eliminate the guesswork in

connecting peripherals to a computer.

VOLT-HOUR INTEGRATOR

The distance at which molecules

migrate in an electrophoresis

apparatus depends on the applied

voltage and run-time (∫V.dt). In order

to achieve reproducible experiments,

it is recommended to use a volt-hour

integrator rather than a simple timer.

ZERO POINT (Eo)

Standard pH meters assume a pH

electrode to supply a zero potential at 7

pH. Electrodes for special applications

(e.g. stomach pH measurements)

may have a different zero point. An

adjustable zero point correction feature

will allow users to measure with these

electrodes.